data_2B8M # _entry.id 2B8M # _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 2B8M pdb_00002b8m 10.2210/pdb2b8m/pdb RCSB RCSB034811 ? ? WWPDB D_1000034811 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 359364 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2B8M _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2005-10-07 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of (1499583) from METHANOCOCCUS JANNASCHII at 1.70 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.length_a 49.830 _cell.length_b 49.830 _cell.length_c 78.740 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 2B8M _cell.pdbx_unique_axis ? _cell.Z_PDB 6 # _symmetry.Int_Tables_number 152 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.entry_id 2B8M _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 'Hypothetical protein MJ0764' 13833.426 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer syn 1,2-ETHANEDIOL 62.068 3 ? ? ? ? 5 water nat water 18.015 132 ? ? ? ? # _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)IEKVYEFKRDAKTKVVEKLVNTEHVQINHIVLPRGEQ(MSE)PKHYSNSYVHLIIIKGE(MSE)TLTLEDQEPH NYKEGNIVYVPFNVK(MSE)LIQNINSDILEFFVVKAPHPKKLNAPEDPIKCE ; _entity_poly.pdbx_seq_one_letter_code_can ;GMIEKVYEFKRDAKTKVVEKLVNTEHVQINHIVLPRGEQMPKHYSNSYVHLIIIKGEMTLTLEDQEPHNYKEGNIVYVPF NVKMLIQNINSDILEFFVVKAPHPKKLNAPEDPIKCE ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 359364 # 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 ILE n 1 4 GLU n 1 5 LYS n 1 6 VAL n 1 7 TYR n 1 8 GLU n 1 9 PHE n 1 10 LYS n 1 11 ARG n 1 12 ASP n 1 13 ALA n 1 14 LYS n 1 15 THR n 1 16 LYS n 1 17 VAL n 1 18 VAL n 1 19 GLU n 1 20 LYS n 1 21 LEU n 1 22 VAL n 1 23 ASN n 1 24 THR n 1 25 GLU n 1 26 HIS n 1 27 VAL n 1 28 GLN n 1 29 ILE n 1 30 ASN n 1 31 HIS n 1 32 ILE n 1 33 VAL n 1 34 LEU n 1 35 PRO n 1 36 ARG n 1 37 GLY n 1 38 GLU n 1 39 GLN n 1 40 MSE n 1 41 PRO n 1 42 LYS n 1 43 HIS n 1 44 TYR n 1 45 SER n 1 46 ASN n 1 47 SER n 1 48 TYR n 1 49 VAL n 1 50 HIS n 1 51 LEU n 1 52 ILE n 1 53 ILE n 1 54 ILE n 1 55 LYS n 1 56 GLY n 1 57 GLU n 1 58 MSE n 1 59 THR n 1 60 LEU n 1 61 THR n 1 62 LEU n 1 63 GLU n 1 64 ASP n 1 65 GLN n 1 66 GLU n 1 67 PRO n 1 68 HIS n 1 69 ASN n 1 70 TYR n 1 71 LYS n 1 72 GLU n 1 73 GLY n 1 74 ASN n 1 75 ILE n 1 76 VAL n 1 77 TYR n 1 78 VAL n 1 79 PRO n 1 80 PHE n 1 81 ASN n 1 82 VAL n 1 83 LYS n 1 84 MSE n 1 85 LEU n 1 86 ILE n 1 87 GLN n 1 88 ASN n 1 89 ILE n 1 90 ASN n 1 91 SER n 1 92 ASP n 1 93 ILE n 1 94 LEU n 1 95 GLU n 1 96 PHE n 1 97 PHE n 1 98 VAL n 1 99 VAL n 1 100 LYS n 1 101 ALA n 1 102 PRO n 1 103 HIS n 1 104 PRO n 1 105 LYS n 1 106 LYS n 1 107 LEU n 1 108 ASN n 1 109 ALA n 1 110 PRO n 1 111 GLU n 1 112 ASP n 1 113 PRO n 1 114 ILE n 1 115 LYS n 1 116 CYS n 1 117 GLU 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 Methanocaldococcus _entity_src_gen.pdbx_gene_src_gene 1499583 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _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 'Methanocaldococcus jannaschii' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2190 _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 Escherichia _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 ? _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 HK100::SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Y764_METJA _struct_ref.pdbx_db_accession Q58174 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MIEKVYEFKRDAKTKVVEKLVNTEHVQINHIVLPRGEQMPKHYSNSYVHLIIIKGEMTLTLEDQEPHNYKEGNIVYVPFN VKMLIQNINSDILEFFVVKAPHPKKLNAPEDPIKCE ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2B8M _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 117 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q58174 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 116 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 116 # 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 2B8M GLY A 1 ? UNP Q58174 ? ? 'expression tag' 0 1 1 2B8M MSE A 2 ? UNP Q58174 MET 1 'modified residue' 1 2 1 2B8M MSE A 40 ? UNP Q58174 MET 39 'modified residue' 39 3 1 2B8M MSE A 58 ? UNP Q58174 MET 57 'modified residue' 57 4 1 2B8M MSE A 84 ? UNP Q58174 MET 83 'modified residue' 83 5 # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 2 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 2B8M # _exptl_crystal.id 1 _exptl_crystal.density_percent_sol 39.7 _exptl_crystal.density_Matthews 1.91 _exptl_crystal.description ? _exptl_crystal.density_meas ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '0.2M (NH4)2SO4, 20.0% PEG-3350, No Buffer, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 6' _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 'ADSC QUANTUM 315' _diffrn_detector.details ? _diffrn_detector.pdbx_collection_date 2005-09-09 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.monochromator 'double crystal Si(111)' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9796 1.0 2 0.9797 1.0 3 1.0000 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9796, 0.9797, 1.0000' _diffrn_source.pdbx_synchrotron_site ALS # _reflns.entry_id 2B8M _reflns.d_resolution_low 29.08 _reflns.d_resolution_high 1.70 _reflns.number_obs 12267 _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs 0.091 _reflns.pdbx_chi_squared ? _reflns.pdbx_redundancy 3.48 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_netI_over_sigmaI 7.840 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all 12925 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_low _reflns_shell.d_res_high _reflns_shell.number_measured_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.number_unique_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.percent_possible_all _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.76 1.70 3933 97.200 0.527 ? ? 2106 2.230 ? 97.2 ? ? 1 1 1.83 1.76 4196 92.600 0.527 ? ? 2224 2.720 ? ? ? ? 2 1 1.91 1.83 4119 94.000 0.527 ? ? 2182 3.570 ? ? ? ? 3 1 2.02 1.91 4705 95.900 0.527 ? ? 2502 4.870 ? ? ? ? 4 1 2.14 2.02 4133 97.000 0.527 ? ? 2198 6.070 ? ? ? ? 5 1 2.31 2.14 4608 97.500 0.527 ? ? 2444 7.390 ? ? ? ? 6 1 2.54 2.31 4421 98.200 0.527 ? ? 2325 9.260 ? ? ? ? 7 1 2.90 2.54 4454 98.800 0.527 ? ? 2352 10.390 ? ? ? ? 8 1 3.66 2.90 4510 99.000 0.527 ? ? 2410 13.240 ? ? ? ? 9 1 29.08 3.66 4475 97.200 0.527 ? ? 2358 17.450 ? ? ? ? 10 1 # _refine.ls_d_res_high 1.700 _refine.ls_d_res_low 29.08 _refine.ls_percent_reflns_obs 99.710 _refine.ls_number_reflns_obs 12267 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.ls_R_factor_all 0.152 _refine.ls_R_factor_R_work 0.149 _refine.ls_R_factor_R_free 0.204 _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 628 _refine.B_iso_mean 20.146 _refine.aniso_B[1][1] 0.590 _refine.aniso_B[2][2] 0.590 _refine.aniso_B[3][3] -0.890 _refine.aniso_B[1][2] 0.300 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.970 _refine.correlation_coeff_Fo_to_Fc_free 0.936 _refine.pdbx_overall_ESU_R 0.094 _refine.pdbx_overall_ESU_R_Free 0.104 _refine.overall_SU_ML 0.067 _refine.overall_SU_B 3.918 _refine.solvent_model_details 'BABINET MODEL WITH 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.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_method_to_determine_struct MAD _refine.entry_id 2B8M _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_obs 0.15197 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ELECTRON DENSITY IS DISORDERED AT THE C-TERMINUS, THEREFORE, THE STRUCTURE WAS NOT MODELED IN THIS REGION 4. ELECTRON DENSITY BETWEEN THE SIDECHAINS OF HIS 25 AND HIS 49 ON SYMMETRY-RELATED SUBUNITS WAS MODELED AS A CHLORIDE ANION ; _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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 886 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 132 _refine_hist.number_atoms_total 1046 _refine_hist.d_res_high 1.700 _refine_hist.d_res_low 29.08 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 941 0.014 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 859 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1272 1.441 1.973 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2011 0.743 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 112 7.208 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 43 32.787 25.581 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 172 10.286 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 2 24.987 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 141 0.092 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1001 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 165 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 129 0.193 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 830 0.180 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 439 0.177 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 581 0.084 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 106 0.174 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 14 0.093 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 49 0.189 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 26 0.155 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 594 2.307 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 221 0.582 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 915 2.690 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 413 5.057 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 356 6.923 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.70 _refine_ls_shell.d_res_low 1.745 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.370 _refine_ls_shell.number_reflns_R_work 893 _refine_ls_shell.R_factor_R_work 0.206 _refine_ls_shell.R_factor_R_free 0.273 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 47 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 2B8M _struct.title ;Crystal structure of a rmlc-like cupin family protein with a double-stranded beta-helix fold (mj0764) from methanocaldococcus jannaschii at 1.70 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function' _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.entry_id 2B8M # 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 2 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 5 ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id HIS _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 103 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ASN _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 108 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id HIS _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 102 _struct_conf.end_auth_comp_id ASN _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 107 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 6 # _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 GLY 1 C ? ? ? 1_555 A MSE 2 N ? ? A GLY 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A ILE 3 N ? ? A MSE 1 A ILE 2 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale3 covale both ? A GLN 39 C ? ? ? 1_555 A MSE 40 N ? ? A GLN 38 A MSE 39 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale4 covale both ? A MSE 40 C ? ? ? 1_555 A PRO 41 N ? ? A MSE 39 A PRO 40 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale5 covale both ? A GLU 57 C ? ? ? 1_555 A MSE 58 N ? ? A GLU 56 A MSE 57 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale6 covale both ? A MSE 58 C ? ? ? 1_555 A THR 59 N ? ? A MSE 57 A THR 58 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale7 covale both ? A LYS 83 C ? ? ? 1_555 A MSE 84 N ? ? A LYS 82 A MSE 83 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale8 covale both ? A MSE 84 C ? ? ? 1_555 A LEU 85 N ? ? A MSE 83 A LEU 84 1_555 ? ? ? ? ? ? ? 1.319 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ALA _struct_mon_prot_cis.label_seq_id 101 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id ALA _struct_mon_prot_cis.auth_seq_id 100 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 102 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 101 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.48 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? 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 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-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 VAL A 17 ? ASN A 23 ? VAL A 16 ASN A 22 A 2 GLN A 28 ? PRO A 35 ? GLN A 27 PRO A 34 A 3 ILE A 93 ? LYS A 100 ? ILE A 92 LYS A 99 A 4 VAL A 49 ? LYS A 55 ? VAL A 48 LYS A 54 A 5 ILE A 75 ? VAL A 78 ? ILE A 74 VAL A 77 B 1 HIS A 43 ? TYR A 44 ? HIS A 42 TYR A 43 B 2 LYS A 83 ? GLN A 87 ? LYS A 82 GLN A 86 B 3 GLU A 57 ? LEU A 62 ? GLU A 56 LEU A 61 B 4 HIS A 68 ? LYS A 71 ? HIS A 67 LYS A 70 # 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 N GLU A 19 ? N GLU A 18 O HIS A 31 ? O HIS A 30 A 2 3 N LEU A 34 ? N LEU A 33 O LEU A 94 ? O LEU A 93 A 3 4 O PHE A 97 ? O PHE A 96 N ILE A 52 ? N ILE A 51 A 4 5 N VAL A 49 ? N VAL A 48 O VAL A 78 ? O VAL A 77 B 1 2 N HIS A 43 ? N HIS A 42 O MSE A 84 ? O MSE A 83 B 2 3 O GLN A 87 ? O GLN A 86 N THR A 59 ? N THR A 58 B 3 4 N MSE A 58 ? N MSE A 57 O TYR A 70 ? O TYR A 69 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 117 ? 9 'BINDING SITE FOR RESIDUE SO4 A 117' AC2 Software A SO4 118 ? 7 'BINDING SITE FOR RESIDUE SO4 A 118' AC3 Software A SO4 119 ? 4 'BINDING SITE FOR RESIDUE SO4 A 119' AC4 Software A CL 120 ? 5 'BINDING SITE FOR RESIDUE CL A 120' AC5 Software A EDO 121 ? 6 'BINDING SITE FOR RESIDUE EDO A 121' AC6 Software A EDO 122 ? 3 'BINDING SITE FOR RESIDUE EDO A 122' AC7 Software A EDO 123 ? 7 'BINDING SITE FOR RESIDUE EDO A 123' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 LYS A 20 ? LYS A 19 . ? 1_555 ? 2 AC1 9 GLN A 28 ? GLN A 27 . ? 1_555 ? 3 AC1 9 ASN A 46 ? ASN A 45 . ? 1_555 ? 4 AC1 9 LYS A 100 ? LYS A 99 . ? 1_555 ? 5 AC1 9 PRO A 104 ? PRO A 103 . ? 1_555 ? 6 AC1 9 HOH I . ? HOH A 207 . ? 1_555 ? 7 AC1 9 HOH I . ? HOH A 226 . ? 1_555 ? 8 AC1 9 HOH I . ? HOH A 234 . ? 1_555 ? 9 AC1 9 HOH I . ? HOH A 241 . ? 1_555 ? 10 AC2 7 TYR A 7 ? TYR A 6 . ? 4_656 ? 11 AC2 7 VAL A 22 ? VAL A 21 . ? 4_656 ? 12 AC2 7 ASN A 23 ? ASN A 22 . ? 4_656 ? 13 AC2 7 LYS A 42 ? LYS A 41 . ? 1_555 ? 14 AC2 7 HOH I . ? HOH A 175 . ? 4_656 ? 15 AC2 7 HOH I . ? HOH A 179 . ? 1_555 ? 16 AC2 7 HOH I . ? HOH A 224 . ? 4_656 ? 17 AC3 4 HIS A 26 ? HIS A 25 . ? 1_555 ? 18 AC3 4 PRO A 102 ? PRO A 101 . ? 5_555 ? 19 AC3 4 HOH I . ? HOH A 135 . ? 1_555 ? 20 AC3 4 HOH I . ? HOH A 153 . ? 1_555 ? 21 AC4 5 THR A 24 ? THR A 23 . ? 1_555 ? 22 AC4 5 HIS A 26 ? HIS A 25 . ? 1_555 ? 23 AC4 5 HIS A 50 ? HIS A 49 . ? 5_555 ? 24 AC4 5 HOH I . ? HOH A 134 . ? 5_555 ? 25 AC4 5 HOH I . ? HOH A 145 . ? 5_555 ? 26 AC5 6 VAL A 17 ? VAL A 16 . ? 1_555 ? 27 AC5 6 VAL A 18 ? VAL A 17 . ? 1_555 ? 28 AC5 6 TYR A 44 ? TYR A 43 . ? 4_546 ? 29 AC5 6 ASN A 81 ? ASN A 80 . ? 4_546 ? 30 AC5 6 HOH I . ? HOH A 196 . ? 1_555 ? 31 AC5 6 HOH I . ? HOH A 222 . ? 1_555 ? 32 AC6 3 GLN A 65 ? GLN A 64 . ? 1_555 ? 33 AC6 3 GLU A 66 ? GLU A 65 . ? 1_555 ? 34 AC6 3 HIS A 68 ? HIS A 67 . ? 1_555 ? 35 AC7 7 HIS A 43 ? HIS A 42 . ? 1_555 ? 36 AC7 7 MSE A 84 ? MSE A 83 . ? 1_555 ? 37 AC7 7 VAL A 98 ? VAL A 97 . ? 1_555 ? 38 AC7 7 HOH I . ? HOH A 151 . ? 1_555 ? 39 AC7 7 HOH I . ? HOH A 155 . ? 1_555 ? 40 AC7 7 HOH I . ? HOH A 219 . ? 1_555 ? 41 AC7 7 HOH I . ? HOH A 246 . ? 1_555 ? # _atom_sites.entry_id 2B8M _atom_sites.fract_transf_matrix[1][1] 0.02007 _atom_sites.fract_transf_matrix[1][2] 0.01159 _atom_sites.fract_transf_matrix[1][3] 0.00000 _atom_sites.fract_transf_matrix[2][1] 0.00000 _atom_sites.fract_transf_matrix[2][2] 0.02317 _atom_sites.fract_transf_matrix[2][3] 0.00000 _atom_sites.fract_transf_matrix[3][1] 0.00000 _atom_sites.fract_transf_matrix[3][2] 0.00000 _atom_sites.fract_transf_matrix[3][3] 0.01270 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL 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 0 GLY GLY A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 ILE 3 2 2 ILE ILE A . n A 1 4 GLU 4 3 3 GLU GLU A . n A 1 5 LYS 5 4 4 LYS LYS A . n A 1 6 VAL 6 5 5 VAL VAL A . n A 1 7 TYR 7 6 6 TYR TYR A . n A 1 8 GLU 8 7 7 GLU GLU A . n A 1 9 PHE 9 8 8 PHE PHE A . n A 1 10 LYS 10 9 9 LYS LYS A . n A 1 11 ARG 11 10 10 ARG ARG A . n A 1 12 ASP 12 11 11 ASP ASP A . n A 1 13 ALA 13 12 12 ALA ALA A . n A 1 14 LYS 14 13 13 LYS LYS A . n A 1 15 THR 15 14 14 THR THR A . n A 1 16 LYS 16 15 15 LYS LYS A . n A 1 17 VAL 17 16 16 VAL VAL A . n A 1 18 VAL 18 17 17 VAL VAL A . n A 1 19 GLU 19 18 18 GLU GLU A . n A 1 20 LYS 20 19 19 LYS LYS A . n A 1 21 LEU 21 20 20 LEU LEU A . n A 1 22 VAL 22 21 21 VAL VAL A . n A 1 23 ASN 23 22 22 ASN ASN A . n A 1 24 THR 24 23 23 THR THR A . n A 1 25 GLU 25 24 24 GLU GLU A . n A 1 26 HIS 26 25 25 HIS HIS A . n A 1 27 VAL 27 26 26 VAL VAL A . n A 1 28 GLN 28 27 27 GLN GLN A . n A 1 29 ILE 29 28 28 ILE ILE A . n A 1 30 ASN 30 29 29 ASN ASN A . n A 1 31 HIS 31 30 30 HIS HIS A . n A 1 32 ILE 32 31 31 ILE ILE A . n A 1 33 VAL 33 32 32 VAL VAL A . n A 1 34 LEU 34 33 33 LEU LEU A . n A 1 35 PRO 35 34 34 PRO PRO A . n A 1 36 ARG 36 35 35 ARG ARG A . n A 1 37 GLY 37 36 36 GLY GLY A . n A 1 38 GLU 38 37 37 GLU GLU A . n A 1 39 GLN 39 38 38 GLN GLN A . n A 1 40 MSE 40 39 39 MSE MSE A . n A 1 41 PRO 41 40 40 PRO PRO A . n A 1 42 LYS 42 41 41 LYS LYS A . n A 1 43 HIS 43 42 42 HIS HIS A . n A 1 44 TYR 44 43 43 TYR TYR A . n A 1 45 SER 45 44 44 SER SER A . n A 1 46 ASN 46 45 45 ASN ASN A . n A 1 47 SER 47 46 46 SER SER A . n A 1 48 TYR 48 47 47 TYR TYR A . n A 1 49 VAL 49 48 48 VAL VAL A . n A 1 50 HIS 50 49 49 HIS HIS A . n A 1 51 LEU 51 50 50 LEU LEU A . n A 1 52 ILE 52 51 51 ILE ILE A . n A 1 53 ILE 53 52 52 ILE ILE A . n A 1 54 ILE 54 53 53 ILE ILE A . n A 1 55 LYS 55 54 54 LYS LYS A . n A 1 56 GLY 56 55 55 GLY GLY A . n A 1 57 GLU 57 56 56 GLU GLU A . n A 1 58 MSE 58 57 57 MSE MSE A . n A 1 59 THR 59 58 58 THR THR A . n A 1 60 LEU 60 59 59 LEU LEU A . n A 1 61 THR 61 60 60 THR THR A . n A 1 62 LEU 62 61 61 LEU LEU A . n A 1 63 GLU 63 62 62 GLU GLU A . n A 1 64 ASP 64 63 63 ASP ASP A . n A 1 65 GLN 65 64 64 GLN GLN A . n A 1 66 GLU 66 65 65 GLU GLU A . n A 1 67 PRO 67 66 66 PRO PRO A . n A 1 68 HIS 68 67 67 HIS HIS A . n A 1 69 ASN 69 68 68 ASN ASN A . n A 1 70 TYR 70 69 69 TYR TYR A . n A 1 71 LYS 71 70 70 LYS LYS A . n A 1 72 GLU 72 71 71 GLU GLU A . n A 1 73 GLY 73 72 72 GLY GLY A . n A 1 74 ASN 74 73 73 ASN ASN A . n A 1 75 ILE 75 74 74 ILE ILE A . n A 1 76 VAL 76 75 75 VAL VAL A . n A 1 77 TYR 77 76 76 TYR TYR A . n A 1 78 VAL 78 77 77 VAL VAL A . n A 1 79 PRO 79 78 78 PRO PRO A . n A 1 80 PHE 80 79 79 PHE PHE A . n A 1 81 ASN 81 80 80 ASN ASN A . n A 1 82 VAL 82 81 81 VAL VAL A . n A 1 83 LYS 83 82 82 LYS LYS A . n A 1 84 MSE 84 83 83 MSE MSE A . n A 1 85 LEU 85 84 84 LEU LEU A . n A 1 86 ILE 86 85 85 ILE ILE A . n A 1 87 GLN 87 86 86 GLN GLN A . n A 1 88 ASN 88 87 87 ASN ASN A . n A 1 89 ILE 89 88 88 ILE ILE A . n A 1 90 ASN 90 89 89 ASN ASN A . n A 1 91 SER 91 90 90 SER SER A . n A 1 92 ASP 92 91 91 ASP ASP A . n A 1 93 ILE 93 92 92 ILE ILE A . n A 1 94 LEU 94 93 93 LEU LEU A . n A 1 95 GLU 95 94 94 GLU GLU A . n A 1 96 PHE 96 95 95 PHE PHE A . n A 1 97 PHE 97 96 96 PHE PHE A . n A 1 98 VAL 98 97 97 VAL VAL A . n A 1 99 VAL 99 98 98 VAL VAL A . n A 1 100 LYS 100 99 99 LYS LYS A . n A 1 101 ALA 101 100 100 ALA ALA A . n A 1 102 PRO 102 101 101 PRO PRO A . n A 1 103 HIS 103 102 102 HIS HIS A . n A 1 104 PRO 104 103 103 PRO PRO A . n A 1 105 LYS 105 104 104 LYS LYS A . n A 1 106 LYS 106 105 105 LYS LYS A . n A 1 107 LEU 107 106 106 LEU LEU A . n A 1 108 ASN 108 107 107 ASN ASN A . n A 1 109 ALA 109 108 108 ALA ALA A . n A 1 110 PRO 110 109 ? ? ? A . n A 1 111 GLU 111 110 ? ? ? A . n A 1 112 ASP 112 111 ? ? ? A . n A 1 113 PRO 113 112 ? ? ? A . n A 1 114 ILE 114 113 ? ? ? A . n A 1 115 LYS 115 114 ? ? ? A . n A 1 116 CYS 116 115 ? ? ? A . n A 1 117 GLU 117 116 ? ? ? A . 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 B 2 SO4 1 117 1 SO4 SO4 A . C 2 SO4 1 118 2 SO4 SO4 A . D 2 SO4 1 119 3 SO4 SO4 A . E 3 CL 1 120 7 CL CL A . F 4 EDO 1 121 4 EDO EDO A . G 4 EDO 1 122 5 EDO EDO A . H 4 EDO 1 123 6 EDO EDO A . I 5 HOH 1 124 8 HOH HOH A . I 5 HOH 2 125 9 HOH HOH A . I 5 HOH 3 126 10 HOH HOH A . I 5 HOH 4 127 11 HOH HOH A . I 5 HOH 5 128 12 HOH HOH A . I 5 HOH 6 129 13 HOH HOH A . I 5 HOH 7 130 14 HOH HOH A . I 5 HOH 8 131 15 HOH HOH A . I 5 HOH 9 132 16 HOH HOH A . I 5 HOH 10 133 17 HOH HOH A . I 5 HOH 11 134 18 HOH HOH A . I 5 HOH 12 135 19 HOH HOH A . I 5 HOH 13 136 20 HOH HOH A . I 5 HOH 14 137 21 HOH HOH A . I 5 HOH 15 138 22 HOH HOH A . I 5 HOH 16 139 23 HOH HOH A . I 5 HOH 17 140 24 HOH HOH A . I 5 HOH 18 141 25 HOH HOH A . I 5 HOH 19 142 26 HOH HOH A . I 5 HOH 20 143 27 HOH HOH A . I 5 HOH 21 144 28 HOH HOH A . I 5 HOH 22 145 29 HOH HOH A . I 5 HOH 23 146 30 HOH HOH A . I 5 HOH 24 147 31 HOH HOH A . I 5 HOH 25 148 32 HOH HOH A . I 5 HOH 26 149 33 HOH HOH A . I 5 HOH 27 150 34 HOH HOH A . I 5 HOH 28 151 35 HOH HOH A . I 5 HOH 29 152 36 HOH HOH A . I 5 HOH 30 153 37 HOH HOH A . I 5 HOH 31 154 38 HOH HOH A . I 5 HOH 32 155 39 HOH HOH A . I 5 HOH 33 156 40 HOH HOH A . I 5 HOH 34 157 41 HOH HOH A . I 5 HOH 35 158 42 HOH HOH A . I 5 HOH 36 159 43 HOH HOH A . I 5 HOH 37 160 44 HOH HOH A . I 5 HOH 38 161 45 HOH HOH A . I 5 HOH 39 162 46 HOH HOH A . I 5 HOH 40 163 47 HOH HOH A . I 5 HOH 41 164 48 HOH HOH A . I 5 HOH 42 165 49 HOH HOH A . I 5 HOH 43 166 50 HOH HOH A . I 5 HOH 44 167 51 HOH HOH A . I 5 HOH 45 168 52 HOH HOH A . I 5 HOH 46 169 53 HOH HOH A . I 5 HOH 47 170 54 HOH HOH A . I 5 HOH 48 171 55 HOH HOH A . I 5 HOH 49 172 56 HOH HOH A . I 5 HOH 50 173 57 HOH HOH A . I 5 HOH 51 174 58 HOH HOH A . I 5 HOH 52 175 59 HOH HOH A . I 5 HOH 53 176 60 HOH HOH A . I 5 HOH 54 177 61 HOH HOH A . I 5 HOH 55 178 62 HOH HOH A . I 5 HOH 56 179 63 HOH HOH A . I 5 HOH 57 180 64 HOH HOH A . I 5 HOH 58 181 65 HOH HOH A . I 5 HOH 59 182 66 HOH HOH A . I 5 HOH 60 183 67 HOH HOH A . I 5 HOH 61 184 68 HOH HOH A . I 5 HOH 62 185 69 HOH HOH A . I 5 HOH 63 186 70 HOH HOH A . I 5 HOH 64 187 71 HOH HOH A . I 5 HOH 65 188 72 HOH HOH A . I 5 HOH 66 189 73 HOH HOH A . I 5 HOH 67 190 74 HOH HOH A . I 5 HOH 68 191 75 HOH HOH A . I 5 HOH 69 192 76 HOH HOH A . I 5 HOH 70 193 77 HOH HOH A . I 5 HOH 71 194 78 HOH HOH A . I 5 HOH 72 195 79 HOH HOH A . I 5 HOH 73 196 80 HOH HOH A . I 5 HOH 74 197 81 HOH HOH A . I 5 HOH 75 198 82 HOH HOH A . I 5 HOH 76 199 83 HOH HOH A . I 5 HOH 77 200 84 HOH HOH A . I 5 HOH 78 201 85 HOH HOH A . I 5 HOH 79 202 86 HOH HOH A . I 5 HOH 80 203 87 HOH HOH A . I 5 HOH 81 204 88 HOH HOH A . I 5 HOH 82 205 89 HOH HOH A . I 5 HOH 83 206 90 HOH HOH A . I 5 HOH 84 207 91 HOH HOH A . I 5 HOH 85 208 92 HOH HOH A . I 5 HOH 86 209 93 HOH HOH A . I 5 HOH 87 210 94 HOH HOH A . I 5 HOH 88 211 95 HOH HOH A . I 5 HOH 89 212 96 HOH HOH A . I 5 HOH 90 213 97 HOH HOH A . I 5 HOH 91 214 98 HOH HOH A . I 5 HOH 92 215 99 HOH HOH A . I 5 HOH 93 216 100 HOH HOH A . I 5 HOH 94 217 101 HOH HOH A . I 5 HOH 95 218 102 HOH HOH A . I 5 HOH 96 219 103 HOH HOH A . I 5 HOH 97 220 104 HOH HOH A . I 5 HOH 98 221 105 HOH HOH A . I 5 HOH 99 222 106 HOH HOH A . I 5 HOH 100 223 107 HOH HOH A . I 5 HOH 101 224 108 HOH HOH A . I 5 HOH 102 225 109 HOH HOH A . I 5 HOH 103 226 110 HOH HOH A . I 5 HOH 104 227 111 HOH HOH A . I 5 HOH 105 228 112 HOH HOH A . I 5 HOH 106 229 113 HOH HOH A . I 5 HOH 107 230 114 HOH HOH A . I 5 HOH 108 231 115 HOH HOH A . I 5 HOH 109 232 116 HOH HOH A . I 5 HOH 110 233 117 HOH HOH A . I 5 HOH 111 234 118 HOH HOH A . I 5 HOH 112 235 119 HOH HOH A . I 5 HOH 113 236 120 HOH HOH A . I 5 HOH 114 237 121 HOH HOH A . I 5 HOH 115 238 122 HOH HOH A . I 5 HOH 116 239 123 HOH HOH A . I 5 HOH 117 240 124 HOH HOH A . I 5 HOH 118 241 125 HOH HOH A . I 5 HOH 119 242 126 HOH HOH A . I 5 HOH 120 243 127 HOH HOH A . I 5 HOH 121 244 128 HOH HOH A . I 5 HOH 122 245 129 HOH HOH A . I 5 HOH 123 246 130 HOH HOH A . I 5 HOH 124 247 131 HOH HOH A . I 5 HOH 125 248 132 HOH HOH A . I 5 HOH 126 249 133 HOH HOH A . I 5 HOH 127 250 134 HOH HOH A . I 5 HOH 128 251 135 HOH HOH A . I 5 HOH 129 252 136 HOH HOH A . I 5 HOH 130 253 137 HOH HOH A . I 5 HOH 131 254 138 HOH HOH A . I 5 HOH 132 255 139 HOH HOH A . # 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 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 40 A MSE 39 ? MET SELENOMETHIONINE 3 A MSE 58 A MSE 57 ? MET SELENOMETHIONINE 4 A MSE 84 A MSE 83 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # 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)' 5980 ? 1 MORE -135 ? 1 'SSA (A^2)' 10130 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 52.4933333333 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 242 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2005-11-01 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-01-25 # _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' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' # 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 4 'Structure model' database_2 2 4 'Structure model' struct_conn 3 4 'Structure model' struct_ref_seq_dif 4 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_ref_seq_dif.details' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 24.9740 _pdbx_refine_tls.origin_y 6.7340 _pdbx_refine_tls.origin_z 32.4560 _pdbx_refine_tls.T[1][1] -0.1405 _pdbx_refine_tls.T[2][2] -0.1147 _pdbx_refine_tls.T[3][3] -0.1250 _pdbx_refine_tls.T[1][2] -0.0009 _pdbx_refine_tls.T[1][3] -0.0016 _pdbx_refine_tls.T[2][3] 0.0032 _pdbx_refine_tls.L[1][1] 0.5384 _pdbx_refine_tls.L[2][2] 1.2481 _pdbx_refine_tls.L[3][3] 0.8392 _pdbx_refine_tls.L[1][2] -0.1081 _pdbx_refine_tls.L[1][3] 0.0201 _pdbx_refine_tls.L[2][3] 0.0566 _pdbx_refine_tls.S[1][1] -0.0138 _pdbx_refine_tls.S[2][2] -0.0001 _pdbx_refine_tls.S[3][3] 0.0139 _pdbx_refine_tls.S[1][2] -0.0747 _pdbx_refine_tls.S[1][3] 0.0532 _pdbx_refine_tls.S[2][3] 0.0272 _pdbx_refine_tls.S[2][1] 0.0865 _pdbx_refine_tls.S[3][1] -0.0396 _pdbx_refine_tls.S[3][2] 0.0059 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 1 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 109 _pdbx_refine_tls_group.selection all _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 0 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 108 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _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 5.2.0005 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran ? 1 XSCALE . ? program 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html ? ? 2 PDB_EXTRACT 1.601 'Jan. 30, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 XDS . ? ? ? ? 'data reduction' ? ? ? 4 SOLVE . ? ? ? ? phasing ? ? ? 5 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ;sequence The construct was expressed with a purification tag MGSDKIHHHHHHENLYFQG. The tag was removed with TEV protease leaving only GLY-0 followed by residues 1-116 of the 1499583 gene target. ; # 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 ASN A 22 ? ? -150.12 81.97 2 1 GLU A 62 ? ? 43.87 -123.96 # 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 LYS 4 ? CE ? A LYS 5 CE 2 1 Y 1 A LYS 4 ? NZ ? A LYS 5 NZ 3 1 Y 1 A LYS 13 ? CE ? A LYS 14 CE 4 1 Y 1 A LYS 13 ? NZ ? A LYS 14 NZ 5 1 Y 1 A LYS 54 ? CE ? A LYS 55 CE 6 1 Y 1 A LYS 54 ? NZ ? A LYS 55 NZ 7 1 Y 1 A ASP 63 ? OD1 ? A ASP 64 OD1 8 1 Y 1 A ASP 63 ? OD2 ? A ASP 64 OD2 9 1 Y 1 A LYS 105 ? NZ ? A LYS 106 NZ # 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 PRO 109 ? A PRO 110 2 1 Y 1 A GLU 110 ? A GLU 111 3 1 Y 1 A ASP 111 ? A ASP 112 4 1 Y 1 A PRO 112 ? A PRO 113 5 1 Y 1 A ILE 113 ? A ILE 114 6 1 Y 1 A LYS 114 ? A LYS 115 7 1 Y 1 A CYS 115 ? A CYS 116 8 1 Y 1 A GLU 116 ? A GLU 117 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 'CHLORIDE ION' CL 4 1,2-ETHANEDIOL EDO 5 water HOH #