data_3LYH # _entry.id 3LYH # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3LYH pdb_00003lyh 10.2210/pdb3lyh/pdb RCSB RCSB057888 ? ? WWPDB D_1000057888 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 403199 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3LYH _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-02-26 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution ; _citation.journal_abbrev 'To be published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 3LYH _cell.length_a 37.836 _cell.length_b 38.615 _cell.length_c 39.845 _cell.angle_alpha 70.350 _cell.angle_beta 83.050 _cell.angle_gamma 72.090 _cell.pdbx_unique_axis ? _cell.Z_PDB 2 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3LYH _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Cobalamin (Vitamin B12) biosynthesis CbiX protein' 14133.674 2 ? ? ? ? 2 water nat water 18.015 217 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;G(MSE)TQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAY(MSE)ELAEPSLDTIVNRAKGQGVEQFTVVPLFL AAGRHLRKDVPA(MSE)IERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH ; _entity_poly.pdbx_seq_one_letter_code_can ;GMTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRK DVPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier 403199 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 MSE n 1 3 THR n 1 4 GLN n 1 5 PRO n 1 6 HIS n 1 7 GLN n 1 8 ILE n 1 9 ILE n 1 10 LEU n 1 11 LEU n 1 12 ALA n 1 13 HIS n 1 14 GLY n 1 15 SER n 1 16 SER n 1 17 ASP n 1 18 ALA n 1 19 ARG n 1 20 TRP n 1 21 CYS n 1 22 GLU n 1 23 THR n 1 24 PHE n 1 25 GLU n 1 26 LYS n 1 27 LEU n 1 28 ALA n 1 29 GLU n 1 30 PRO n 1 31 THR n 1 32 VAL n 1 33 GLU n 1 34 SER n 1 35 ILE n 1 36 GLU n 1 37 ASN n 1 38 ALA n 1 39 ALA n 1 40 ILE n 1 41 ALA n 1 42 TYR n 1 43 MSE n 1 44 GLU n 1 45 LEU n 1 46 ALA n 1 47 GLU n 1 48 PRO n 1 49 SER n 1 50 LEU n 1 51 ASP n 1 52 THR n 1 53 ILE n 1 54 VAL n 1 55 ASN n 1 56 ARG n 1 57 ALA n 1 58 LYS n 1 59 GLY n 1 60 GLN n 1 61 GLY n 1 62 VAL n 1 63 GLU n 1 64 GLN n 1 65 PHE n 1 66 THR n 1 67 VAL n 1 68 VAL n 1 69 PRO n 1 70 LEU n 1 71 PHE n 1 72 LEU n 1 73 ALA n 1 74 ALA n 1 75 GLY n 1 76 ARG n 1 77 HIS n 1 78 LEU n 1 79 ARG n 1 80 LYS n 1 81 ASP n 1 82 VAL n 1 83 PRO n 1 84 ALA n 1 85 MSE n 1 86 ILE n 1 87 GLU n 1 88 ARG n 1 89 LEU n 1 90 GLU n 1 91 ALA n 1 92 GLU n 1 93 HIS n 1 94 GLY n 1 95 VAL n 1 96 THR n 1 97 ILE n 1 98 ARG n 1 99 LEU n 1 100 ALA n 1 101 GLU n 1 102 PRO n 1 103 ILE n 1 104 GLY n 1 105 LYS n 1 106 ASN n 1 107 PRO n 1 108 ARG n 1 109 LEU n 1 110 GLY n 1 111 LEU n 1 112 ALA n 1 113 ILE n 1 114 ARG n 1 115 ASP n 1 116 VAL n 1 117 VAL n 1 118 LYS n 1 119 GLU n 1 120 GLU n 1 121 LEU n 1 122 GLU n 1 123 ARG n 1 124 SER n 1 125 GLU n 1 126 HIS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Maqu_1136 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 700491 / DSM 11845 / VT8' _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Marinobacter aquaeolei' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 351348 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain HK100 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A1TZQ9_MARAV _struct_ref.pdbx_db_accession A1TZQ9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRKD VPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3LYH A 2 ? 126 ? A1TZQ9 1 ? 125 ? 1 125 2 1 3LYH B 2 ? 126 ? A1TZQ9 1 ? 125 ? 1 125 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3LYH GLY A 1 ? UNP A1TZQ9 ? ? 'expression tag' 0 1 2 3LYH GLY B 1 ? UNP A1TZQ9 ? ? 'expression tag' 0 2 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3LYH # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.85 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 33.34 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat collimating mirror, toroid focusing mirror' _diffrn_detector.pdbx_collection_date 2010-01-23 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double crystal monochromator' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.97915 1.0 2 0.97903 1.0 3 0.91162 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL9-2 _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list 0.97915,0.97903,0.91162 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3LYH _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 29.618 _reflns.number_all ? _reflns.number_obs 25860 _reflns.pdbx_Rsym_value 0.054 _reflns.pdbx_redundancy 3.300 _reflns.percent_possible_obs 96.700 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 3LYH _refine.ls_d_res_high 1.600 _refine.ls_d_res_low 29.618 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.460 _refine.ls_number_reflns_obs 25860 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.172 _refine.ls_R_factor_R_work 0.170 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.209 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 1291 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 19.754 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.070 _refine.aniso_B[2][2] 1.130 _refine.aniso_B[3][3] -0.020 _refine.aniso_B[1][2] -1.080 _refine.aniso_B[1][3] 1.110 _refine.aniso_B[2][3] -1.160 _refine.correlation_coeff_Fo_to_Fc 0.966 _refine.correlation_coeff_Fo_to_Fc_free 0.952 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.103 _refine.pdbx_overall_ESU_R_Free 0.102 _refine.overall_SU_ML 0.065 _refine.overall_SU_B 4.121 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 60.53 _refine.B_iso_min 2.43 _refine.occupancy_max 1.00 _refine.occupancy_min 0.30 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1837 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 217 _refine_hist.number_atoms_total 2054 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 29.618 # loop_ _refine_ls_restr.type _refine_ls_restr.pdbx_refine_id _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 'X-RAY DIFFRACTION' 1983 0.016 0.022 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 1339 0.002 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 2716 1.645 1.977 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 3303 1.151 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 272 6.166 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 86 36.175 24.419 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 348 13.339 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 14 16.660 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 319 0.097 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 2237 0.007 0.021 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 374 0.001 0.020 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 1262 1.918 3.000 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 503 0.527 3.000 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 2044 3.135 5.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 721 5.390 8.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 657 8.550 11.000 ? ? # _refine_ls_shell.d_res_high 1.597 _refine_ls_shell.d_res_low 1.639 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 91.580 _refine_ls_shell.number_reflns_R_work 1729 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.252 _refine_ls_shell.R_factor_R_free 0.231 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 77 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1806 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3LYH _struct.title ;Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Putative cobalamin (vitamin B12) biosynthesis CbiX protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, LYASE ; _struct_keywords.pdbx_keywords LYASE _struct_keywords.entry_id 3LYH # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 ASP A 17 ? ILE A 35 ? ASP A 16 ILE A 34 1 ? 19 HELX_P HELX_P2 2 SER A 49 ? GLN A 60 ? SER A 48 GLN A 59 1 ? 12 HELX_P HELX_P3 3 GLY A 75 ? GLY A 94 ? GLY A 74 GLY A 93 1 ? 20 HELX_P HELX_P4 4 PRO A 102 ? LYS A 105 ? PRO A 101 LYS A 104 5 ? 4 HELX_P HELX_P5 5 ASN A 106 ? SER A 124 ? ASN A 105 SER A 123 1 ? 19 HELX_P HELX_P6 6 ASP B 17 ? ILE B 35 ? ASP B 16 ILE B 34 1 ? 19 HELX_P HELX_P7 7 SER B 49 ? GLN B 60 ? SER B 48 GLN B 59 1 ? 12 HELX_P HELX_P8 8 HIS B 77 ? GLY B 94 ? HIS B 76 GLY B 93 1 ? 18 HELX_P HELX_P9 9 PRO B 102 ? LYS B 105 ? PRO B 101 LYS B 104 5 ? 4 HELX_P HELX_P10 10 ASN B 106 ? HIS B 126 ? ASN B 105 HIS B 125 1 ? 21 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A TYR 42 C ? ? ? 1_555 A MSE 43 N ? ? A TYR 41 A MSE 42 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale2 covale both ? A MSE 43 C ? ? ? 1_555 A GLU 44 N ? ? A MSE 42 A GLU 43 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale3 covale both ? A ALA 84 C ? ? ? 1_555 A MSE 85 N ? ? A ALA 83 A MSE 84 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale4 covale both ? A MSE 85 C ? ? ? 1_555 A ILE 86 N ? ? A MSE 84 A ILE 85 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale5 covale both ? B TYR 42 C ? ? ? 1_555 B MSE 43 N ? ? B TYR 41 B MSE 42 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale6 covale both ? B MSE 43 C ? ? ? 1_555 B GLU 44 N ? ? B MSE 42 B GLU 43 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale7 covale both ? B ALA 84 C ? ? ? 1_555 B MSE 85 N ? ? B ALA 83 B MSE 84 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale8 covale both ? B MSE 85 C ? ? ? 1_555 B ILE 86 N ? ? B MSE 84 B ILE 85 1_555 ? ? ? ? ? ? ? 1.339 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 GLU 47 A . ? GLU 46 A PRO 48 A ? PRO 47 A 1 -0.32 2 GLN 4 B . ? GLN 3 B PRO 5 B ? PRO 4 B 1 -22.75 3 GLU 47 B . ? GLU 46 B PRO 48 B ? PRO 47 B 1 2.63 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? parallel A 2 3 ? parallel A 3 4 ? parallel B 1 2 ? parallel B 2 3 ? parallel B 3 4 ? parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ALA A 39 ? TYR A 42 ? ALA A 38 TYR A 41 A 2 HIS A 6 ? ALA A 12 ? HIS A 5 ALA A 11 A 3 GLN A 64 ? PRO A 69 ? GLN A 63 PRO A 68 A 4 THR A 96 ? LEU A 99 ? THR A 95 LEU A 98 B 1 ALA B 38 ? TYR B 42 ? ALA B 37 TYR B 41 B 2 HIS B 6 ? ALA B 12 ? HIS B 5 ALA B 11 B 3 GLN B 64 ? PRO B 69 ? GLN B 63 PRO B 68 B 4 THR B 96 ? LEU B 99 ? THR B 95 LEU B 98 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ALA A 41 ? O ALA A 40 N ALA A 12 ? N ALA A 11 A 2 3 N ILE A 9 ? N ILE A 8 O VAL A 68 ? O VAL A 67 A 3 4 N VAL A 67 ? N VAL A 66 O ARG A 98 ? O ARG A 97 B 1 2 O ALA B 39 ? O ALA B 38 N LEU B 10 ? N LEU B 9 B 2 3 N ILE B 9 ? N ILE B 8 O VAL B 68 ? O VAL B 67 B 3 4 N VAL B 67 ? N VAL B 66 O ARG B 98 ? O ARG B 97 # _atom_sites.entry_id 3LYH _atom_sites.fract_transf_matrix[1][1] 0.026430 _atom_sites.fract_transf_matrix[1][2] -0.008543 _atom_sites.fract_transf_matrix[1][3] -0.000546 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.027216 _atom_sites.fract_transf_matrix[2][3] -0.009086 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.026655 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 ? ? ? A . n A 1 3 THR 3 2 ? ? ? A . n A 1 4 GLN 4 3 ? ? ? A . n A 1 5 PRO 5 4 4 PRO PRO A . n A 1 6 HIS 6 5 5 HIS HIS A . n A 1 7 GLN 7 6 6 GLN GLN A . n A 1 8 ILE 8 7 7 ILE ILE A . n A 1 9 ILE 9 8 8 ILE ILE A . n A 1 10 LEU 10 9 9 LEU LEU A . n A 1 11 LEU 11 10 10 LEU LEU A . n A 1 12 ALA 12 11 11 ALA ALA A . n A 1 13 HIS 13 12 12 HIS HIS A . n A 1 14 GLY 14 13 13 GLY GLY A . n A 1 15 SER 15 14 14 SER SER A . n A 1 16 SER 16 15 15 SER SER A . n A 1 17 ASP 17 16 16 ASP ASP A . n A 1 18 ALA 18 17 17 ALA ALA A . n A 1 19 ARG 19 18 18 ARG ARG A . n A 1 20 TRP 20 19 19 TRP TRP A . n A 1 21 CYS 21 20 20 CYS CYS A . n A 1 22 GLU 22 21 21 GLU GLU A . n A 1 23 THR 23 22 22 THR THR A . n A 1 24 PHE 24 23 23 PHE PHE A . n A 1 25 GLU 25 24 24 GLU GLU A . n A 1 26 LYS 26 25 25 LYS LYS A . n A 1 27 LEU 27 26 26 LEU LEU A . n A 1 28 ALA 28 27 27 ALA ALA A . n A 1 29 GLU 29 28 28 GLU GLU A . n A 1 30 PRO 30 29 29 PRO PRO A . n A 1 31 THR 31 30 30 THR THR A . n A 1 32 VAL 32 31 31 VAL VAL A . n A 1 33 GLU 33 32 32 GLU GLU A . n A 1 34 SER 34 33 33 SER SER A . n A 1 35 ILE 35 34 34 ILE ILE A . n A 1 36 GLU 36 35 35 GLU GLU A . n A 1 37 ASN 37 36 36 ASN ASN A . n A 1 38 ALA 38 37 37 ALA ALA A . n A 1 39 ALA 39 38 38 ALA ALA A . n A 1 40 ILE 40 39 39 ILE ILE A . n A 1 41 ALA 41 40 40 ALA ALA A . n A 1 42 TYR 42 41 41 TYR TYR A . n A 1 43 MSE 43 42 42 MSE MSE A . n A 1 44 GLU 44 43 43 GLU GLU A . n A 1 45 LEU 45 44 44 LEU LEU A . n A 1 46 ALA 46 45 45 ALA ALA A . n A 1 47 GLU 47 46 46 GLU GLU A . n A 1 48 PRO 48 47 47 PRO PRO A . n A 1 49 SER 49 48 48 SER SER A . n A 1 50 LEU 50 49 49 LEU LEU A . n A 1 51 ASP 51 50 50 ASP ASP A . n A 1 52 THR 52 51 51 THR THR A . n A 1 53 ILE 53 52 52 ILE ILE A . n A 1 54 VAL 54 53 53 VAL VAL A . n A 1 55 ASN 55 54 54 ASN ASN A . n A 1 56 ARG 56 55 55 ARG ARG A . n A 1 57 ALA 57 56 56 ALA ALA A . n A 1 58 LYS 58 57 57 LYS LYS A . n A 1 59 GLY 59 58 58 GLY GLY A . n A 1 60 GLN 60 59 59 GLN GLN A . n A 1 61 GLY 61 60 60 GLY GLY A . n A 1 62 VAL 62 61 61 VAL VAL A . n A 1 63 GLU 63 62 62 GLU GLU A . n A 1 64 GLN 64 63 63 GLN GLN A . n A 1 65 PHE 65 64 64 PHE PHE A . n A 1 66 THR 66 65 65 THR THR A . n A 1 67 VAL 67 66 66 VAL VAL A . n A 1 68 VAL 68 67 67 VAL VAL A . n A 1 69 PRO 69 68 68 PRO PRO A . n A 1 70 LEU 70 69 69 LEU LEU A . n A 1 71 PHE 71 70 70 PHE PHE A . n A 1 72 LEU 72 71 71 LEU LEU A . n A 1 73 ALA 73 72 72 ALA ALA A . n A 1 74 ALA 74 73 73 ALA ALA A . n A 1 75 GLY 75 74 74 GLY GLY A . n A 1 76 ARG 76 75 75 ARG ARG A . n A 1 77 HIS 77 76 76 HIS HIS A . n A 1 78 LEU 78 77 77 LEU LEU A . n A 1 79 ARG 79 78 78 ARG ARG A . n A 1 80 LYS 80 79 79 LYS LYS A . n A 1 81 ASP 81 80 80 ASP ASP A . n A 1 82 VAL 82 81 81 VAL VAL A . n A 1 83 PRO 83 82 82 PRO PRO A . n A 1 84 ALA 84 83 83 ALA ALA A . n A 1 85 MSE 85 84 84 MSE MSE A . n A 1 86 ILE 86 85 85 ILE ILE A . n A 1 87 GLU 87 86 86 GLU GLU A . n A 1 88 ARG 88 87 87 ARG ARG A . n A 1 89 LEU 89 88 88 LEU LEU A . n A 1 90 GLU 90 89 89 GLU GLU A . n A 1 91 ALA 91 90 90 ALA ALA A . n A 1 92 GLU 92 91 91 GLU GLU A . n A 1 93 HIS 93 92 92 HIS HIS A . n A 1 94 GLY 94 93 93 GLY GLY A . n A 1 95 VAL 95 94 94 VAL VAL A . n A 1 96 THR 96 95 95 THR THR A . n A 1 97 ILE 97 96 96 ILE ILE A . n A 1 98 ARG 98 97 97 ARG ARG A . n A 1 99 LEU 99 98 98 LEU LEU A . n A 1 100 ALA 100 99 99 ALA ALA A . n A 1 101 GLU 101 100 100 GLU GLU A . n A 1 102 PRO 102 101 101 PRO PRO A . n A 1 103 ILE 103 102 102 ILE ILE A . n A 1 104 GLY 104 103 103 GLY GLY A . n A 1 105 LYS 105 104 104 LYS LYS A . n A 1 106 ASN 106 105 105 ASN ASN A . n A 1 107 PRO 107 106 106 PRO PRO A . n A 1 108 ARG 108 107 107 ARG ARG A . n A 1 109 LEU 109 108 108 LEU LEU A . n A 1 110 GLY 110 109 109 GLY GLY A . n A 1 111 LEU 111 110 110 LEU LEU A . n A 1 112 ALA 112 111 111 ALA ALA A . n A 1 113 ILE 113 112 112 ILE ILE A . n A 1 114 ARG 114 113 113 ARG ARG A . n A 1 115 ASP 115 114 114 ASP ASP A . n A 1 116 VAL 116 115 115 VAL VAL A . n A 1 117 VAL 117 116 116 VAL VAL A . n A 1 118 LYS 118 117 117 LYS LYS A . n A 1 119 GLU 119 118 118 GLU GLU A . n A 1 120 GLU 120 119 119 GLU GLU A . n A 1 121 LEU 121 120 120 LEU LEU A . n A 1 122 GLU 122 121 121 GLU GLU A . n A 1 123 ARG 123 122 122 ARG ARG A . n A 1 124 SER 124 123 123 SER SER A . n A 1 125 GLU 125 124 ? ? ? A . n A 1 126 HIS 126 125 ? ? ? A . n B 1 1 GLY 1 0 ? ? ? B . n B 1 2 MSE 2 1 ? ? ? B . n B 1 3 THR 3 2 ? ? ? B . n B 1 4 GLN 4 3 3 GLN GLN B . n B 1 5 PRO 5 4 4 PRO PRO B . n B 1 6 HIS 6 5 5 HIS HIS B . n B 1 7 GLN 7 6 6 GLN GLN B . n B 1 8 ILE 8 7 7 ILE ILE B . n B 1 9 ILE 9 8 8 ILE ILE B . n B 1 10 LEU 10 9 9 LEU LEU B . n B 1 11 LEU 11 10 10 LEU LEU B . n B 1 12 ALA 12 11 11 ALA ALA B . n B 1 13 HIS 13 12 12 HIS HIS B . n B 1 14 GLY 14 13 13 GLY GLY B . n B 1 15 SER 15 14 14 SER SER B . n B 1 16 SER 16 15 15 SER SER B . n B 1 17 ASP 17 16 16 ASP ASP B . n B 1 18 ALA 18 17 17 ALA ALA B . n B 1 19 ARG 19 18 18 ARG ARG B . n B 1 20 TRP 20 19 19 TRP TRP B . n B 1 21 CYS 21 20 20 CYS CYS B . n B 1 22 GLU 22 21 21 GLU GLU B . n B 1 23 THR 23 22 22 THR THR B . n B 1 24 PHE 24 23 23 PHE PHE B . n B 1 25 GLU 25 24 24 GLU GLU B . n B 1 26 LYS 26 25 25 LYS LYS B . n B 1 27 LEU 27 26 26 LEU LEU B . n B 1 28 ALA 28 27 27 ALA ALA B . n B 1 29 GLU 29 28 28 GLU GLU B . n B 1 30 PRO 30 29 29 PRO PRO B . n B 1 31 THR 31 30 30 THR THR B . n B 1 32 VAL 32 31 31 VAL VAL B . n B 1 33 GLU 33 32 32 GLU GLU B . n B 1 34 SER 34 33 33 SER SER B . n B 1 35 ILE 35 34 34 ILE ILE B . n B 1 36 GLU 36 35 35 GLU GLU B . n B 1 37 ASN 37 36 36 ASN ASN B . n B 1 38 ALA 38 37 37 ALA ALA B . n B 1 39 ALA 39 38 38 ALA ALA B . n B 1 40 ILE 40 39 39 ILE ILE B . n B 1 41 ALA 41 40 40 ALA ALA B . n B 1 42 TYR 42 41 41 TYR TYR B . n B 1 43 MSE 43 42 42 MSE MSE B . n B 1 44 GLU 44 43 43 GLU GLU B . n B 1 45 LEU 45 44 44 LEU LEU B . n B 1 46 ALA 46 45 45 ALA ALA B . n B 1 47 GLU 47 46 46 GLU GLU B . n B 1 48 PRO 48 47 47 PRO PRO B . n B 1 49 SER 49 48 48 SER SER B . n B 1 50 LEU 50 49 49 LEU LEU B . n B 1 51 ASP 51 50 50 ASP ASP B . n B 1 52 THR 52 51 51 THR THR B . n B 1 53 ILE 53 52 52 ILE ILE B . n B 1 54 VAL 54 53 53 VAL VAL B . n B 1 55 ASN 55 54 54 ASN ASN B . n B 1 56 ARG 56 55 55 ARG ARG B . n B 1 57 ALA 57 56 56 ALA ALA B . n B 1 58 LYS 58 57 57 LYS LYS B . n B 1 59 GLY 59 58 58 GLY GLY B . n B 1 60 GLN 60 59 59 GLN GLN B . n B 1 61 GLY 61 60 60 GLY GLY B . n B 1 62 VAL 62 61 61 VAL VAL B . n B 1 63 GLU 63 62 62 GLU GLU B . n B 1 64 GLN 64 63 63 GLN GLN B . n B 1 65 PHE 65 64 64 PHE PHE B . n B 1 66 THR 66 65 65 THR THR B . n B 1 67 VAL 67 66 66 VAL VAL B . n B 1 68 VAL 68 67 67 VAL VAL B . n B 1 69 PRO 69 68 68 PRO PRO B . n B 1 70 LEU 70 69 69 LEU LEU B . n B 1 71 PHE 71 70 70 PHE PHE B . n B 1 72 LEU 72 71 71 LEU LEU B . n B 1 73 ALA 73 72 72 ALA ALA B . n B 1 74 ALA 74 73 73 ALA ALA B . n B 1 75 GLY 75 74 74 GLY GLY B . n B 1 76 ARG 76 75 ? ? ? B . n B 1 77 HIS 77 76 76 HIS HIS B . n B 1 78 LEU 78 77 77 LEU LEU B . n B 1 79 ARG 79 78 78 ARG ARG B . n B 1 80 LYS 80 79 79 LYS LYS B . n B 1 81 ASP 81 80 80 ASP ASP B . n B 1 82 VAL 82 81 81 VAL VAL B . n B 1 83 PRO 83 82 82 PRO PRO B . n B 1 84 ALA 84 83 83 ALA ALA B . n B 1 85 MSE 85 84 84 MSE MSE B . n B 1 86 ILE 86 85 85 ILE ILE B . n B 1 87 GLU 87 86 86 GLU GLU B . n B 1 88 ARG 88 87 87 ARG ARG B . n B 1 89 LEU 89 88 88 LEU LEU B . n B 1 90 GLU 90 89 89 GLU GLU B . n B 1 91 ALA 91 90 90 ALA ALA B . n B 1 92 GLU 92 91 91 GLU GLU B . n B 1 93 HIS 93 92 92 HIS HIS B . n B 1 94 GLY 94 93 93 GLY GLY B . n B 1 95 VAL 95 94 94 VAL VAL B . n B 1 96 THR 96 95 95 THR THR B . n B 1 97 ILE 97 96 96 ILE ILE B . n B 1 98 ARG 98 97 97 ARG ARG B . n B 1 99 LEU 99 98 98 LEU LEU B . n B 1 100 ALA 100 99 99 ALA ALA B . n B 1 101 GLU 101 100 100 GLU GLU B . n B 1 102 PRO 102 101 101 PRO PRO B . n B 1 103 ILE 103 102 102 ILE ILE B . n B 1 104 GLY 104 103 103 GLY GLY B . n B 1 105 LYS 105 104 104 LYS LYS B . n B 1 106 ASN 106 105 105 ASN ASN B . n B 1 107 PRO 107 106 106 PRO PRO B . n B 1 108 ARG 108 107 107 ARG ARG B . n B 1 109 LEU 109 108 108 LEU LEU B . n B 1 110 GLY 110 109 109 GLY GLY B . n B 1 111 LEU 111 110 110 LEU LEU B . n B 1 112 ALA 112 111 111 ALA ALA B . n B 1 113 ILE 113 112 112 ILE ILE B . n B 1 114 ARG 114 113 113 ARG ARG B . n B 1 115 ASP 115 114 114 ASP ASP B . n B 1 116 VAL 116 115 115 VAL VAL B . n B 1 117 VAL 117 116 116 VAL VAL B . n B 1 118 LYS 118 117 117 LYS LYS B . n B 1 119 GLU 119 118 118 GLU GLU B . n B 1 120 GLU 120 119 119 GLU GLU B . n B 1 121 LEU 121 120 120 LEU LEU B . n B 1 122 GLU 122 121 121 GLU GLU B . n B 1 123 ARG 123 122 122 ARG ARG B . n B 1 124 SER 124 123 123 SER SER B . n B 1 125 GLU 125 124 124 GLU GLU B . n B 1 126 HIS 126 125 125 HIS HIS B . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 126 126 HOH HOH A . C 2 HOH 2 127 127 HOH HOH A . C 2 HOH 3 128 128 HOH HOH A . C 2 HOH 4 129 2 HOH HOH A . C 2 HOH 5 130 130 HOH HOH A . C 2 HOH 6 131 4 HOH HOH A . C 2 HOH 7 132 132 HOH HOH A . C 2 HOH 8 133 133 HOH HOH A . C 2 HOH 9 134 5 HOH HOH A . C 2 HOH 10 135 135 HOH HOH A . C 2 HOH 11 136 136 HOH HOH A . C 2 HOH 12 137 137 HOH HOH A . C 2 HOH 13 138 138 HOH HOH A . C 2 HOH 14 139 139 HOH HOH A . C 2 HOH 15 140 7 HOH HOH A . C 2 HOH 16 141 8 HOH HOH A . C 2 HOH 17 142 142 HOH HOH A . C 2 HOH 18 143 9 HOH HOH A . C 2 HOH 19 144 144 HOH HOH A . C 2 HOH 20 145 10 HOH HOH A . C 2 HOH 21 146 146 HOH HOH A . C 2 HOH 22 147 147 HOH HOH A . C 2 HOH 23 148 148 HOH HOH A . C 2 HOH 24 149 12 HOH HOH A . C 2 HOH 25 150 150 HOH HOH A . C 2 HOH 26 151 151 HOH HOH A . C 2 HOH 27 152 14 HOH HOH A . C 2 HOH 28 153 15 HOH HOH A . C 2 HOH 29 154 19 HOH HOH A . C 2 HOH 30 155 155 HOH HOH A . C 2 HOH 31 156 156 HOH HOH A . C 2 HOH 32 157 24 HOH HOH A . C 2 HOH 33 158 25 HOH HOH A . C 2 HOH 34 159 26 HOH HOH A . C 2 HOH 35 160 28 HOH HOH A . C 2 HOH 36 161 161 HOH HOH A . C 2 HOH 37 162 162 HOH HOH A . C 2 HOH 38 163 29 HOH HOH A . C 2 HOH 39 164 31 HOH HOH A . C 2 HOH 40 165 165 HOH HOH A . C 2 HOH 41 166 36 HOH HOH A . C 2 HOH 42 167 167 HOH HOH A . C 2 HOH 43 168 40 HOH HOH A . C 2 HOH 44 169 169 HOH HOH A . C 2 HOH 45 170 48 HOH HOH A . C 2 HOH 46 171 49 HOH HOH A . C 2 HOH 47 172 51 HOH HOH A . C 2 HOH 48 173 52 HOH HOH A . C 2 HOH 49 174 174 HOH HOH A . C 2 HOH 50 175 175 HOH HOH A . C 2 HOH 51 176 54 HOH HOH A . C 2 HOH 52 177 55 HOH HOH A . C 2 HOH 53 178 56 HOH HOH A . C 2 HOH 54 179 179 HOH HOH A . C 2 HOH 55 180 180 HOH HOH A . C 2 HOH 56 181 181 HOH HOH A . C 2 HOH 57 182 182 HOH HOH A . C 2 HOH 58 183 183 HOH HOH A . C 2 HOH 59 184 184 HOH HOH A . C 2 HOH 60 185 59 HOH HOH A . C 2 HOH 61 186 186 HOH HOH A . C 2 HOH 62 187 63 HOH HOH A . C 2 HOH 63 188 64 HOH HOH A . C 2 HOH 64 189 66 HOH HOH A . C 2 HOH 65 190 67 HOH HOH A . C 2 HOH 66 191 69 HOH HOH A . C 2 HOH 67 192 70 HOH HOH A . C 2 HOH 68 193 71 HOH HOH A . C 2 HOH 69 194 194 HOH HOH A . C 2 HOH 70 195 195 HOH HOH A . C 2 HOH 71 196 196 HOH HOH A . C 2 HOH 72 197 197 HOH HOH A . C 2 HOH 73 198 74 HOH HOH A . C 2 HOH 74 199 75 HOH HOH A . C 2 HOH 75 200 76 HOH HOH A . C 2 HOH 76 201 201 HOH HOH A . C 2 HOH 77 202 202 HOH HOH A . C 2 HOH 78 203 77 HOH HOH A . C 2 HOH 79 204 204 HOH HOH A . C 2 HOH 80 205 205 HOH HOH A . C 2 HOH 81 206 206 HOH HOH A . C 2 HOH 82 207 207 HOH HOH A . C 2 HOH 83 208 208 HOH HOH A . C 2 HOH 84 209 80 HOH HOH A . C 2 HOH 85 210 210 HOH HOH A . C 2 HOH 86 211 81 HOH HOH A . C 2 HOH 87 212 85 HOH HOH A . C 2 HOH 88 213 213 HOH HOH A . C 2 HOH 89 214 214 HOH HOH A . C 2 HOH 90 215 88 HOH HOH A . C 2 HOH 91 216 216 HOH HOH A . C 2 HOH 92 217 217 HOH HOH A . C 2 HOH 93 218 89 HOH HOH A . C 2 HOH 94 219 90 HOH HOH A . C 2 HOH 95 220 93 HOH HOH A . C 2 HOH 96 221 95 HOH HOH A . C 2 HOH 97 222 96 HOH HOH A . C 2 HOH 98 223 98 HOH HOH A . C 2 HOH 99 224 100 HOH HOH A . C 2 HOH 100 225 101 HOH HOH A . C 2 HOH 101 226 103 HOH HOH A . C 2 HOH 102 227 105 HOH HOH A . C 2 HOH 103 228 108 HOH HOH A . C 2 HOH 104 229 109 HOH HOH A . C 2 HOH 105 230 110 HOH HOH A . C 2 HOH 106 231 111 HOH HOH A . C 2 HOH 107 232 114 HOH HOH A . C 2 HOH 108 233 116 HOH HOH A . C 2 HOH 109 234 117 HOH HOH A . C 2 HOH 110 235 118 HOH HOH A . C 2 HOH 111 236 122 HOH HOH A . C 2 HOH 112 237 123 HOH HOH A . C 2 HOH 113 238 125 HOH HOH A . D 2 HOH 1 126 1 HOH HOH B . D 2 HOH 2 127 3 HOH HOH B . D 2 HOH 3 128 6 HOH HOH B . D 2 HOH 4 129 129 HOH HOH B . D 2 HOH 5 130 11 HOH HOH B . D 2 HOH 6 131 131 HOH HOH B . D 2 HOH 7 132 13 HOH HOH B . D 2 HOH 8 133 16 HOH HOH B . D 2 HOH 9 134 134 HOH HOH B . D 2 HOH 10 135 17 HOH HOH B . D 2 HOH 11 136 18 HOH HOH B . D 2 HOH 12 137 20 HOH HOH B . D 2 HOH 13 138 21 HOH HOH B . D 2 HOH 14 139 22 HOH HOH B . D 2 HOH 15 140 140 HOH HOH B . D 2 HOH 16 141 141 HOH HOH B . D 2 HOH 17 142 23 HOH HOH B . D 2 HOH 18 143 143 HOH HOH B . D 2 HOH 19 144 27 HOH HOH B . D 2 HOH 20 145 145 HOH HOH B . D 2 HOH 21 146 30 HOH HOH B . D 2 HOH 22 147 32 HOH HOH B . D 2 HOH 23 148 33 HOH HOH B . D 2 HOH 24 149 149 HOH HOH B . D 2 HOH 25 150 34 HOH HOH B . D 2 HOH 26 151 35 HOH HOH B . D 2 HOH 27 152 152 HOH HOH B . D 2 HOH 28 153 153 HOH HOH B . D 2 HOH 29 154 154 HOH HOH B . D 2 HOH 30 155 37 HOH HOH B . D 2 HOH 31 156 38 HOH HOH B . D 2 HOH 32 157 157 HOH HOH B . D 2 HOH 33 158 158 HOH HOH B . D 2 HOH 34 159 159 HOH HOH B . D 2 HOH 35 160 160 HOH HOH B . D 2 HOH 36 161 39 HOH HOH B . D 2 HOH 37 162 41 HOH HOH B . D 2 HOH 38 163 163 HOH HOH B . D 2 HOH 39 164 164 HOH HOH B . D 2 HOH 40 165 42 HOH HOH B . D 2 HOH 41 166 166 HOH HOH B . D 2 HOH 42 167 43 HOH HOH B . D 2 HOH 43 168 168 HOH HOH B . D 2 HOH 44 169 44 HOH HOH B . D 2 HOH 45 170 170 HOH HOH B . D 2 HOH 46 171 171 HOH HOH B . D 2 HOH 47 172 172 HOH HOH B . D 2 HOH 48 173 173 HOH HOH B . D 2 HOH 49 174 45 HOH HOH B . D 2 HOH 50 175 46 HOH HOH B . D 2 HOH 51 176 176 HOH HOH B . D 2 HOH 52 177 177 HOH HOH B . D 2 HOH 53 178 178 HOH HOH B . D 2 HOH 54 179 47 HOH HOH B . D 2 HOH 55 180 50 HOH HOH B . D 2 HOH 56 181 53 HOH HOH B . D 2 HOH 57 182 57 HOH HOH B . D 2 HOH 58 183 58 HOH HOH B . D 2 HOH 59 184 60 HOH HOH B . D 2 HOH 60 185 185 HOH HOH B . D 2 HOH 61 186 61 HOH HOH B . D 2 HOH 62 187 187 HOH HOH B . D 2 HOH 63 188 188 HOH HOH B . D 2 HOH 64 189 189 HOH HOH B . D 2 HOH 65 190 190 HOH HOH B . D 2 HOH 66 191 191 HOH HOH B . D 2 HOH 67 192 192 HOH HOH B . D 2 HOH 68 193 193 HOH HOH B . D 2 HOH 69 194 62 HOH HOH B . D 2 HOH 70 195 65 HOH HOH B . D 2 HOH 71 196 68 HOH HOH B . D 2 HOH 72 197 72 HOH HOH B . D 2 HOH 73 198 198 HOH HOH B . D 2 HOH 74 199 199 HOH HOH B . D 2 HOH 75 200 200 HOH HOH B . D 2 HOH 76 201 73 HOH HOH B . D 2 HOH 77 202 78 HOH HOH B . D 2 HOH 78 203 203 HOH HOH B . D 2 HOH 79 204 79 HOH HOH B . D 2 HOH 80 205 82 HOH HOH B . D 2 HOH 81 206 83 HOH HOH B . D 2 HOH 82 207 84 HOH HOH B . D 2 HOH 83 208 86 HOH HOH B . D 2 HOH 84 209 209 HOH HOH B . D 2 HOH 85 210 87 HOH HOH B . D 2 HOH 86 211 211 HOH HOH B . D 2 HOH 87 212 212 HOH HOH B . D 2 HOH 88 213 91 HOH HOH B . D 2 HOH 89 214 92 HOH HOH B . D 2 HOH 90 215 215 HOH HOH B . D 2 HOH 91 216 94 HOH HOH B . D 2 HOH 92 217 97 HOH HOH B . D 2 HOH 93 218 99 HOH HOH B . D 2 HOH 94 219 102 HOH HOH B . D 2 HOH 95 220 104 HOH HOH B . D 2 HOH 96 221 106 HOH HOH B . D 2 HOH 97 222 107 HOH HOH B . D 2 HOH 98 223 112 HOH HOH B . D 2 HOH 99 224 113 HOH HOH B . D 2 HOH 100 225 115 HOH HOH B . D 2 HOH 101 226 119 HOH HOH B . D 2 HOH 102 227 120 HOH HOH B . D 2 HOH 103 228 121 HOH HOH B . D 2 HOH 104 229 124 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 43 A MSE 42 ? MET SELENOMETHIONINE 2 A MSE 85 A MSE 84 ? MET SELENOMETHIONINE 3 B MSE 43 B MSE 42 ? MET SELENOMETHIONINE 4 B MSE 85 B MSE 84 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4150 ? 1 MORE -30 ? 1 'SSA (A^2)' 11340 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2010-04-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2019-07-17 5 'Structure model' 1 4 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' software 3 4 'Structure model' struct_conn 4 5 'Structure model' database_2 5 5 'Structure model' struct_ref_seq_dif # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 43.7798 33.6772 7.6424 0.0133 0.0150 0.0141 0.0097 0.0024 0.0025 0.5134 0.6021 1.3116 -0.0765 -0.0744 0.5339 0.0552 -0.0138 -0.0414 0.0504 -0.0094 -0.0205 0.0255 0.0567 0.0637 'X-RAY DIFFRACTION' 2 ? refined 34.0782 48.4636 19.2297 0.0172 0.0121 0.0282 -0.0009 -0.0051 0.0056 0.6571 0.5340 1.0500 0.1883 0.2532 0.6019 -0.0482 -0.0246 0.0728 -0.0020 0.0908 0.0282 0.0107 -0.0381 -0.0396 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 4 A 123 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 3 B 125 ? . . . . ? # _phasing.method MAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.5.0102 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 SCALA 3.3.15 2009/03/31 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 5 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 autoSHARP . ? ? ? ? phasing ? ? ? 9 # _pdbx_entry_details.entry_id 3LYH _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 NE _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 78 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CZ _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 78 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 NH1 _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 78 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 123.38 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation 3.08 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 LEU A 44 ? ? 73.10 -24.93 2 1 LEU B 44 ? ? 63.36 -11.73 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A PRO 4 ? CG ? A PRO 5 CG 2 1 Y 1 A PRO 4 ? CD ? A PRO 5 CD 3 1 Y 1 A GLU 35 ? CG ? A GLU 36 CG 4 1 Y 1 A GLU 35 ? CD ? A GLU 36 CD 5 1 Y 1 A GLU 35 ? OE1 ? A GLU 36 OE1 6 1 Y 1 A GLU 35 ? OE2 ? A GLU 36 OE2 7 1 Y 1 A ARG 75 ? CD ? A ARG 76 CD 8 1 Y 1 A ARG 75 ? NE ? A ARG 76 NE 9 1 Y 1 A ARG 75 ? CZ ? A ARG 76 CZ 10 1 Y 1 A ARG 75 ? NH1 ? A ARG 76 NH1 11 1 Y 1 A ARG 75 ? NH2 ? A ARG 76 NH2 12 1 Y 1 A GLU 121 ? CG ? A GLU 122 CG 13 1 Y 1 A GLU 121 ? CD ? A GLU 122 CD 14 1 Y 1 A GLU 121 ? OE1 ? A GLU 122 OE1 15 1 Y 1 A GLU 121 ? OE2 ? A GLU 122 OE2 16 1 Y 1 A ARG 122 ? CG ? A ARG 123 CG 17 1 Y 1 A ARG 122 ? CD ? A ARG 123 CD 18 1 Y 1 A ARG 122 ? NE ? A ARG 123 NE 19 1 Y 1 A ARG 122 ? CZ ? A ARG 123 CZ 20 1 Y 1 A ARG 122 ? NH1 ? A ARG 123 NH1 21 1 Y 1 A ARG 122 ? NH2 ? A ARG 123 NH2 22 1 Y 1 B GLN 3 ? CG ? B GLN 4 CG 23 1 Y 1 B GLN 3 ? CD ? B GLN 4 CD 24 1 Y 1 B GLN 3 ? OE1 ? B GLN 4 OE1 25 1 Y 1 B GLN 3 ? NE2 ? B GLN 4 NE2 26 1 Y 1 B ARG 18 ? CD ? B ARG 19 CD 27 1 Y 1 B ARG 18 ? NE ? B ARG 19 NE 28 1 Y 1 B ARG 18 ? CZ ? B ARG 19 CZ 29 1 Y 1 B ARG 18 ? NH1 ? B ARG 19 NH1 30 1 Y 1 B ARG 18 ? NH2 ? B ARG 19 NH2 31 1 Y 1 B LYS 25 ? CD ? B LYS 26 CD 32 1 Y 1 B LYS 25 ? CE ? B LYS 26 CE 33 1 Y 1 B LYS 25 ? NZ ? B LYS 26 NZ 34 1 Y 1 B HIS 76 ? CG ? B HIS 77 CG 35 1 Y 1 B HIS 76 ? ND1 ? B HIS 77 ND1 36 1 Y 1 B HIS 76 ? CD2 ? B HIS 77 CD2 37 1 Y 1 B HIS 76 ? CE1 ? B HIS 77 CE1 38 1 Y 1 B HIS 76 ? NE2 ? B HIS 77 NE2 39 1 Y 1 B LEU 77 ? CG ? B LEU 78 CG 40 1 Y 1 B LEU 77 ? CD1 ? B LEU 78 CD1 41 1 Y 1 B LEU 77 ? CD2 ? B LEU 78 CD2 42 1 Y 1 B LYS 79 ? CD ? B LYS 80 CD 43 1 Y 1 B LYS 79 ? CE ? B LYS 80 CE 44 1 Y 1 B LYS 79 ? NZ ? B LYS 80 NZ 45 1 Y 1 B HIS 125 ? CG ? B HIS 126 CG 46 1 Y 1 B HIS 125 ? ND1 ? B HIS 126 ND1 47 1 Y 1 B HIS 125 ? CD2 ? B HIS 126 CD2 48 1 Y 1 B HIS 125 ? CE1 ? B HIS 126 CE1 49 1 Y 1 B HIS 125 ? NE2 ? B HIS 126 NE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A MSE 1 ? A MSE 2 3 1 Y 1 A THR 2 ? A THR 3 4 1 Y 1 A GLN 3 ? A GLN 4 5 1 Y 1 A GLU 124 ? A GLU 125 6 1 Y 1 A HIS 125 ? A HIS 126 7 1 Y 1 B GLY 0 ? B GLY 1 8 1 Y 1 B MSE 1 ? B MSE 2 9 1 Y 1 B THR 2 ? B THR 3 10 1 Y 1 B ARG 75 ? B ARG 76 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #