data_3LYG # _entry.id 3LYG # _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 3LYG pdb_00003lyg 10.2210/pdb3lyg/pdb RCSB RCSB057887 ? ? WWPDB D_1000057887 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 402769 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3LYG _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 NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 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 3LYG _cell.length_a 57.387 _cell.length_b 57.387 _cell.length_c 67.339 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 3LYG _symmetry.Int_Tables_number 96 _symmetry.space_group_name_H-M 'P 43 21 2' _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 'NTF2-like protein of unknown function' 13862.056 1 ? ? ? ? 2 non-polymer syn IMIDAZOLE 69.085 1 ? ? ? ? 3 non-polymer syn 'UNKNOWN LIGAND' ? 1 ? ? ? ? 4 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 5 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 6 water nat water 18.015 150 ? ? ? ? # _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)NLANIVQRGWEALGAGDFDTLVTDYVEK(MSE)IFI(MSE)PGQADVLKGRQAFRSALDNLGEILPPGFEITGL RQLEGENEIVSIVEWKSDK(MSE)IASQLSVLFKFEGDQIYEERWFVDTEQWKSVF ; _entity_poly.pdbx_seq_one_letter_code_can ;GMNLANIVQRGWEALGAGDFDTLVTDYVEKMIFIMPGQADVLKGRQAFRSALDNLGEILPPGFEITGLRQLEGENEIVSI VEWKSDKMIASQLSVLFKFEGDQIYEERWFVDTEQWKSVF ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 402769 # 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 ASN n 1 4 LEU n 1 5 ALA n 1 6 ASN n 1 7 ILE n 1 8 VAL n 1 9 GLN n 1 10 ARG n 1 11 GLY n 1 12 TRP n 1 13 GLU n 1 14 ALA n 1 15 LEU n 1 16 GLY n 1 17 ALA n 1 18 GLY n 1 19 ASP n 1 20 PHE n 1 21 ASP n 1 22 THR n 1 23 LEU n 1 24 VAL n 1 25 THR n 1 26 ASP n 1 27 TYR n 1 28 VAL n 1 29 GLU n 1 30 LYS n 1 31 MSE n 1 32 ILE n 1 33 PHE n 1 34 ILE n 1 35 MSE n 1 36 PRO n 1 37 GLY n 1 38 GLN n 1 39 ALA n 1 40 ASP n 1 41 VAL n 1 42 LEU n 1 43 LYS n 1 44 GLY n 1 45 ARG n 1 46 GLN n 1 47 ALA n 1 48 PHE n 1 49 ARG n 1 50 SER n 1 51 ALA n 1 52 LEU n 1 53 ASP n 1 54 ASN n 1 55 LEU n 1 56 GLY n 1 57 GLU n 1 58 ILE n 1 59 LEU n 1 60 PRO n 1 61 PRO n 1 62 GLY n 1 63 PHE n 1 64 GLU n 1 65 ILE n 1 66 THR n 1 67 GLY n 1 68 LEU n 1 69 ARG n 1 70 GLN n 1 71 LEU n 1 72 GLU n 1 73 GLY n 1 74 GLU n 1 75 ASN n 1 76 GLU n 1 77 ILE n 1 78 VAL n 1 79 SER n 1 80 ILE n 1 81 VAL n 1 82 GLU n 1 83 TRP n 1 84 LYS n 1 85 SER n 1 86 ASP n 1 87 LYS n 1 88 MSE n 1 89 ILE n 1 90 ALA n 1 91 SER n 1 92 GLN n 1 93 LEU n 1 94 SER n 1 95 VAL n 1 96 LEU n 1 97 PHE n 1 98 LYS n 1 99 PHE n 1 100 GLU n 1 101 GLY n 1 102 ASP n 1 103 GLN n 1 104 ILE n 1 105 TYR n 1 106 GLU n 1 107 GLU n 1 108 ARG n 1 109 TRP n 1 110 PHE n 1 111 VAL n 1 112 ASP n 1 113 THR n 1 114 GLU n 1 115 GLN n 1 116 TRP n 1 117 LYS n 1 118 SER n 1 119 VAL n 1 120 PHE 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 CPS_3947 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain '34H / ATCC BAA-681' _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 'Colwellia psychrerythraea' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 167879 _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 Q47X65_COLP3 _struct_ref.pdbx_db_accession Q47X65 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MNLANIVQRGWEALGAGDFDTLVTDYVEKMIFIMPGQADVLKGRQAFRSALDNLGEILPPGFEITGLRQLEGENEIVSIV EWKSDKMIASQLSVLFKFEGDQIYEERWFVDTEQWKSVF ; _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 3LYG _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 120 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q47X65 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 119 _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 119 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3LYG _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q47X65 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 IMD non-polymer . IMIDAZOLE ? 'C3 H5 N2 1' 69.085 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 UNL non-polymer . 'UNKNOWN LIGAND' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3LYG # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.00 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 38.49 _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 9.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '3.2000M (NH4)2SO4, 0.1M Bicine pH 9.0, 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 mirror (vertical focusing)' _diffrn_detector.pdbx_collection_date 2009-12-03 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (horizontal focusing)' _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 0.91837 1.0 2 0.97925 1.0 3 0.97901 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.91837,0.97925,0.97901 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3LYG _reflns.d_resolution_high 1.61 _reflns.d_resolution_low 67.335 _reflns.number_all ? _reflns.number_obs 15075 _reflns.pdbx_Rsym_value 0.095 _reflns.pdbx_redundancy 6.900 _reflns.percent_possible_obs 100.000 _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 15.570 _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 3LYG _refine.ls_d_res_high 1.610 _refine.ls_d_res_low 67.335 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.930 _refine.ls_number_reflns_obs 15033 _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. 4. AN IMIDAZOLE WAS MODELED IN THE ACTIVE SITE. A BENZOIC ACID LIKE MOLECULE WAS MODELED AS UNL. SULFATE (SO4) AND GLYCEROL (GOL) MODELEED WERE WERE PRESENT IN CRYTALLIZATION/CRYO CONDITIONS. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.152 _refine.ls_R_factor_R_work 0.151 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.181 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 758 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 15.581 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.450 _refine.aniso_B[2][2] -0.450 _refine.aniso_B[3][3] 0.900 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.967 _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 0.088 _refine.pdbx_overall_ESU_R_Free 0.086 _refine.overall_SU_ML 0.052 _refine.overall_SU_B 3.292 _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 60.62 _refine.B_iso_min 4.54 _refine.occupancy_max 1.00 _refine.occupancy_min 0.15 _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 964 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 25 _refine_hist.number_atoms_solvent 150 _refine_hist.number_atoms_total 1139 _refine_hist.d_res_high 1.610 _refine_hist.d_res_low 67.335 # 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' 1065 0.017 0.022 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 733 0.002 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 1444 1.528 1.978 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 1793 0.914 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 134 5.970 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 54 35.433 25.556 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 193 11.484 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 5 12.638 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 152 0.101 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 1189 0.008 0.020 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 217 0.001 0.020 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 619 1.726 3.000 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 255 0.497 3.000 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 1002 2.545 5.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 446 4.007 8.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 434 5.896 11.000 ? ? # _refine_ls_shell.d_res_high 1.614 _refine_ls_shell.d_res_low 1.656 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.730 _refine_ls_shell.number_reflns_R_work 1033 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.234 _refine_ls_shell.R_factor_R_free 0.283 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 56 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1089 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3LYG _struct.title 'Crystal structure of NTF2-like protein of unknown function (YP_270605.1) from Colwellia psychrerythraea 34H at 1.61 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 'Structural Genomics, Unknown function' _struct_keywords.entry_id 3LYG # 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 3 ? D N N 4 ? E N N 5 ? F N N 6 ? # _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 ASN A 3 ? GLY A 18 ? ASN A 2 GLY A 17 1 ? 16 HELX_P HELX_P2 2 ASP A 19 ? VAL A 24 ? ASP A 18 VAL A 23 1 ? 6 HELX_P HELX_P3 3 GLY A 44 ? ASP A 53 ? GLY A 43 ASP A 52 1 ? 10 HELX_P HELX_P4 4 ASN A 54 ? LEU A 59 ? ASN A 53 LEU A 58 1 ? 6 HELX_P HELX_P5 5 ASP A 112 ? VAL A 119 ? ASP A 111 VAL A 118 1 ? 8 # _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 ? ? ? ? ? ? ? 1.326 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A ASN 3 N ? ? A MSE 1 A ASN 2 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale3 covale both ? A LYS 30 C ? ? ? 1_555 A MSE 31 N ? ? A LYS 29 A MSE 30 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale4 covale both ? A MSE 31 C ? ? ? 1_555 A ILE 32 N ? ? A MSE 30 A ILE 31 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale5 covale both ? A ILE 34 C ? ? ? 1_555 A MSE 35 N ? ? A ILE 33 A MSE 34 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale6 covale both ? A MSE 35 C ? ? ? 1_555 A PRO 36 N ? ? A MSE 34 A PRO 35 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale7 covale both ? A LYS 87 C ? ? ? 1_555 A MSE 88 N ? ? A LYS 86 A MSE 87 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale8 covale both ? A MSE 88 C ? ? ? 1_555 A ILE 89 N ? ? A MSE 87 A ILE 88 1_555 ? ? ? ? ? ? ? 1.326 ? ? # _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 MSE _struct_mon_prot_cis.label_seq_id 35 _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 MSE _struct_mon_prot_cis.auth_seq_id 34 _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 36 _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 35 _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 3.39 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _struct_sheet.details ? # 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 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? 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 41 ? LYS A 43 ? VAL A 40 LYS A 42 A 2 TYR A 27 ? ILE A 34 ? TYR A 26 ILE A 33 A 3 GLN A 103 ? PHE A 110 ? GLN A 102 PHE A 109 A 4 MSE A 88 ? GLU A 100 ? MSE A 87 GLU A 99 A 5 GLU A 76 ? SER A 85 ? GLU A 75 SER A 84 A 6 GLU A 64 ? GLU A 72 ? GLU A 63 GLU A 71 # 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 LEU A 42 ? O LEU A 41 N PHE A 33 ? N PHE A 32 A 2 3 N ILE A 34 ? N ILE A 33 O GLU A 107 ? O GLU A 106 A 3 4 O GLN A 103 ? O GLN A 102 N GLU A 100 ? N GLU A 99 A 4 5 O PHE A 97 ? O PHE A 96 N ILE A 77 ? N ILE A 76 A 5 6 O VAL A 78 ? O VAL A 77 N LEU A 71 ? N LEU A 70 # 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 IMD 120 ? 7 'BINDING SITE FOR RESIDUE IMD A 120' AC2 Software A SO4 122 ? 6 'BINDING SITE FOR RESIDUE SO4 A 122' AC3 Software A GOL 123 ? 8 'BINDING SITE FOR RESIDUE GOL 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 7 VAL A 8 ? VAL A 7 . ? 1_555 ? 2 AC1 7 GLY A 11 ? GLY A 10 . ? 1_555 ? 3 AC1 7 TRP A 12 ? TRP A 11 . ? 1_555 ? 4 AC1 7 TYR A 27 ? TYR A 26 . ? 1_555 ? 5 AC1 7 PHE A 97 ? PHE A 96 . ? 1_555 ? 6 AC1 7 HOH F . ? HOH A 167 . ? 1_555 ? 7 AC1 7 HOH F . ? HOH A 175 . ? 1_555 ? 8 AC2 6 LYS A 43 ? LYS A 42 . ? 5_545 ? 9 AC2 6 THR A 66 ? THR A 65 . ? 1_555 ? 10 AC2 6 LYS A 84 ? LYS A 83 . ? 1_555 ? 11 AC2 6 HOH F . ? HOH A 135 . ? 1_555 ? 12 AC2 6 HOH F . ? HOH A 150 . ? 5_545 ? 13 AC2 6 HOH F . ? HOH A 208 . ? 1_555 ? 14 AC3 8 GLU A 29 ? GLU A 28 . ? 1_555 ? 15 AC3 8 LYS A 43 ? LYS A 42 . ? 1_555 ? 16 AC3 8 GLY A 44 ? GLY A 43 . ? 1_555 ? 17 AC3 8 ARG A 45 ? ARG A 44 . ? 1_555 ? 18 AC3 8 GLN A 46 ? GLN A 45 . ? 1_555 ? 19 AC3 8 ALA A 47 ? ALA A 46 . ? 1_555 ? 20 AC3 8 HOH F . ? HOH A 204 . ? 1_555 ? 21 AC3 8 HOH F . ? HOH A 210 . ? 3_554 ? # _atom_sites.entry_id 3LYG _atom_sites.fract_transf_matrix[1][1] 0.017426 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.017426 _atom_sites.fract_transf_matrix[2][3] 0.000000 _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] 0.014850 _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 0 GLY GLY A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 ASN 3 2 2 ASN ASN A . n A 1 4 LEU 4 3 3 LEU LEU A . n A 1 5 ALA 5 4 4 ALA ALA A . n A 1 6 ASN 6 5 5 ASN ASN A . n A 1 7 ILE 7 6 6 ILE ILE A . n A 1 8 VAL 8 7 7 VAL VAL A . n A 1 9 GLN 9 8 8 GLN GLN A . n A 1 10 ARG 10 9 9 ARG ARG A . n A 1 11 GLY 11 10 10 GLY GLY A . n A 1 12 TRP 12 11 11 TRP TRP A . n A 1 13 GLU 13 12 12 GLU GLU A . n A 1 14 ALA 14 13 13 ALA ALA A . n A 1 15 LEU 15 14 14 LEU LEU A . n A 1 16 GLY 16 15 15 GLY GLY A . n A 1 17 ALA 17 16 16 ALA ALA A . n A 1 18 GLY 18 17 17 GLY GLY A . n A 1 19 ASP 19 18 18 ASP ASP A . n A 1 20 PHE 20 19 19 PHE PHE A . n A 1 21 ASP 21 20 20 ASP ASP A . n A 1 22 THR 22 21 21 THR THR A . n A 1 23 LEU 23 22 22 LEU LEU A . n A 1 24 VAL 24 23 23 VAL VAL A . n A 1 25 THR 25 24 24 THR THR A . n A 1 26 ASP 26 25 25 ASP ASP A . n A 1 27 TYR 27 26 26 TYR TYR A . n A 1 28 VAL 28 27 27 VAL VAL A . n A 1 29 GLU 29 28 28 GLU GLU A . n A 1 30 LYS 30 29 29 LYS LYS A . n A 1 31 MSE 31 30 30 MSE MSE A . n A 1 32 ILE 32 31 31 ILE ILE A . n A 1 33 PHE 33 32 32 PHE PHE A . n A 1 34 ILE 34 33 33 ILE ILE A . n A 1 35 MSE 35 34 34 MSE MSE A . n A 1 36 PRO 36 35 35 PRO PRO A . n A 1 37 GLY 37 36 36 GLY GLY A . n A 1 38 GLN 38 37 37 GLN GLN A . n A 1 39 ALA 39 38 38 ALA ALA A . n A 1 40 ASP 40 39 39 ASP ASP A . n A 1 41 VAL 41 40 40 VAL VAL A . n A 1 42 LEU 42 41 41 LEU LEU A . n A 1 43 LYS 43 42 42 LYS LYS A . n A 1 44 GLY 44 43 43 GLY GLY A . n A 1 45 ARG 45 44 44 ARG ARG A . n A 1 46 GLN 46 45 45 GLN GLN A . n A 1 47 ALA 47 46 46 ALA ALA A . n A 1 48 PHE 48 47 47 PHE PHE A . n A 1 49 ARG 49 48 48 ARG ARG A . n A 1 50 SER 50 49 49 SER SER A . n A 1 51 ALA 51 50 50 ALA ALA A . n A 1 52 LEU 52 51 51 LEU LEU A . n A 1 53 ASP 53 52 52 ASP ASP A . n A 1 54 ASN 54 53 53 ASN ASN A . n A 1 55 LEU 55 54 54 LEU LEU 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 ILE 58 57 57 ILE ILE A . n A 1 59 LEU 59 58 58 LEU LEU A . n A 1 60 PRO 60 59 59 PRO PRO A . n A 1 61 PRO 61 60 60 PRO PRO A . n A 1 62 GLY 62 61 61 GLY GLY A . n A 1 63 PHE 63 62 62 PHE PHE A . n A 1 64 GLU 64 63 63 GLU GLU A . n A 1 65 ILE 65 64 64 ILE ILE A . n A 1 66 THR 66 65 65 THR THR A . n A 1 67 GLY 67 66 66 GLY GLY A . n A 1 68 LEU 68 67 67 LEU LEU A . n A 1 69 ARG 69 68 68 ARG ARG A . n A 1 70 GLN 70 69 69 GLN GLN A . n A 1 71 LEU 71 70 70 LEU LEU 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 GLU 74 73 73 GLU GLU A . n A 1 75 ASN 75 74 74 ASN ASN A . n A 1 76 GLU 76 75 75 GLU GLU A . n A 1 77 ILE 77 76 76 ILE ILE A . n A 1 78 VAL 78 77 77 VAL VAL A . n A 1 79 SER 79 78 78 SER SER A . n A 1 80 ILE 80 79 79 ILE ILE A . n A 1 81 VAL 81 80 80 VAL VAL A . n A 1 82 GLU 82 81 81 GLU GLU A . n A 1 83 TRP 83 82 82 TRP TRP A . n A 1 84 LYS 84 83 83 LYS LYS A . n A 1 85 SER 85 84 84 SER SER A . n A 1 86 ASP 86 85 85 ASP ASP A . n A 1 87 LYS 87 86 86 LYS LYS A . n A 1 88 MSE 88 87 87 MSE MSE A . n A 1 89 ILE 89 88 88 ILE ILE A . n A 1 90 ALA 90 89 89 ALA ALA A . n A 1 91 SER 91 90 90 SER SER A . n A 1 92 GLN 92 91 91 GLN GLN A . n A 1 93 LEU 93 92 92 LEU LEU A . n A 1 94 SER 94 93 93 SER SER A . n A 1 95 VAL 95 94 94 VAL VAL A . n A 1 96 LEU 96 95 95 LEU LEU A . n A 1 97 PHE 97 96 96 PHE PHE A . n A 1 98 LYS 98 97 97 LYS LYS A . n A 1 99 PHE 99 98 98 PHE PHE A . n A 1 100 GLU 100 99 99 GLU GLU A . n A 1 101 GLY 101 100 100 GLY GLY A . n A 1 102 ASP 102 101 101 ASP ASP A . n A 1 103 GLN 103 102 102 GLN GLN A . n A 1 104 ILE 104 103 103 ILE ILE A . n A 1 105 TYR 105 104 104 TYR TYR A . n A 1 106 GLU 106 105 105 GLU GLU A . n A 1 107 GLU 107 106 106 GLU GLU A . n A 1 108 ARG 108 107 107 ARG ARG A . n A 1 109 TRP 109 108 108 TRP TRP A . n A 1 110 PHE 110 109 109 PHE PHE A . n A 1 111 VAL 111 110 110 VAL VAL A . n A 1 112 ASP 112 111 111 ASP ASP A . n A 1 113 THR 113 112 112 THR THR A . n A 1 114 GLU 114 113 113 GLU GLU A . n A 1 115 GLN 115 114 114 GLN GLN A . n A 1 116 TRP 116 115 115 TRP TRP A . n A 1 117 LYS 117 116 116 LYS LYS A . n A 1 118 SER 118 117 117 SER SER A . n A 1 119 VAL 119 118 118 VAL VAL A . n A 1 120 PHE 120 119 119 PHE PHE 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 IMD 1 120 1 IMD IMD A . C 3 UNL 1 121 2 UNL UNL A . D 4 SO4 1 122 3 SO4 SO4 A . E 5 GOL 1 123 4 GOL GOL A . F 6 HOH 1 124 124 HOH HOH A . F 6 HOH 2 125 125 HOH HOH A . F 6 HOH 3 126 126 HOH HOH A . F 6 HOH 4 127 127 HOH HOH A . F 6 HOH 5 128 128 HOH HOH A . F 6 HOH 6 129 129 HOH HOH A . F 6 HOH 7 130 130 HOH HOH A . F 6 HOH 8 131 131 HOH HOH A . F 6 HOH 9 132 132 HOH HOH A . F 6 HOH 10 133 133 HOH HOH A . F 6 HOH 11 134 134 HOH HOH A . F 6 HOH 12 135 135 HOH HOH A . F 6 HOH 13 136 136 HOH HOH A . F 6 HOH 14 137 137 HOH HOH A . F 6 HOH 15 138 138 HOH HOH A . F 6 HOH 16 139 139 HOH HOH A . F 6 HOH 17 140 140 HOH HOH A . F 6 HOH 18 141 141 HOH HOH A . F 6 HOH 19 142 142 HOH HOH A . F 6 HOH 20 143 143 HOH HOH A . F 6 HOH 21 144 144 HOH HOH A . F 6 HOH 22 145 145 HOH HOH A . F 6 HOH 23 146 146 HOH HOH A . F 6 HOH 24 147 147 HOH HOH A . F 6 HOH 25 148 148 HOH HOH A . F 6 HOH 26 149 149 HOH HOH A . F 6 HOH 27 150 150 HOH HOH A . F 6 HOH 28 151 151 HOH HOH A . F 6 HOH 29 152 152 HOH HOH A . F 6 HOH 30 153 153 HOH HOH A . F 6 HOH 31 154 154 HOH HOH A . F 6 HOH 32 155 5 HOH HOH A . F 6 HOH 33 156 6 HOH HOH A . F 6 HOH 34 157 7 HOH HOH A . F 6 HOH 35 158 8 HOH HOH A . F 6 HOH 36 159 9 HOH HOH A . F 6 HOH 37 160 10 HOH HOH A . F 6 HOH 38 161 11 HOH HOH A . F 6 HOH 39 162 12 HOH HOH A . F 6 HOH 40 163 13 HOH HOH A . F 6 HOH 41 164 14 HOH HOH A . F 6 HOH 42 165 15 HOH HOH A . F 6 HOH 43 166 16 HOH HOH A . F 6 HOH 44 167 17 HOH HOH A . F 6 HOH 45 168 18 HOH HOH A . F 6 HOH 46 169 19 HOH HOH A . F 6 HOH 47 170 20 HOH HOH A . F 6 HOH 48 171 21 HOH HOH A . F 6 HOH 49 172 22 HOH HOH A . F 6 HOH 50 173 23 HOH HOH A . F 6 HOH 51 174 24 HOH HOH A . F 6 HOH 52 175 25 HOH HOH A . F 6 HOH 53 176 26 HOH HOH A . F 6 HOH 54 177 27 HOH HOH A . F 6 HOH 55 178 28 HOH HOH A . F 6 HOH 56 179 29 HOH HOH A . F 6 HOH 57 180 30 HOH HOH A . F 6 HOH 58 181 31 HOH HOH A . F 6 HOH 59 182 32 HOH HOH A . F 6 HOH 60 183 33 HOH HOH A . F 6 HOH 61 184 34 HOH HOH A . F 6 HOH 62 185 35 HOH HOH A . F 6 HOH 63 186 36 HOH HOH A . F 6 HOH 64 187 37 HOH HOH A . F 6 HOH 65 188 38 HOH HOH A . F 6 HOH 66 189 39 HOH HOH A . F 6 HOH 67 190 40 HOH HOH A . F 6 HOH 68 191 41 HOH HOH A . F 6 HOH 69 192 42 HOH HOH A . F 6 HOH 70 193 43 HOH HOH A . F 6 HOH 71 194 44 HOH HOH A . F 6 HOH 72 195 45 HOH HOH A . F 6 HOH 73 196 46 HOH HOH A . F 6 HOH 74 197 47 HOH HOH A . F 6 HOH 75 198 48 HOH HOH A . F 6 HOH 76 199 49 HOH HOH A . F 6 HOH 77 200 50 HOH HOH A . F 6 HOH 78 201 51 HOH HOH A . F 6 HOH 79 202 52 HOH HOH A . F 6 HOH 80 203 53 HOH HOH A . F 6 HOH 81 204 54 HOH HOH A . F 6 HOH 82 205 55 HOH HOH A . F 6 HOH 83 206 56 HOH HOH A . F 6 HOH 84 207 57 HOH HOH A . F 6 HOH 85 208 58 HOH HOH A . F 6 HOH 86 209 59 HOH HOH A . F 6 HOH 87 210 60 HOH HOH A . F 6 HOH 88 211 61 HOH HOH A . F 6 HOH 89 212 62 HOH HOH A . F 6 HOH 90 213 63 HOH HOH A . F 6 HOH 91 214 64 HOH HOH A . F 6 HOH 92 215 65 HOH HOH A . F 6 HOH 93 216 66 HOH HOH A . F 6 HOH 94 217 67 HOH HOH A . F 6 HOH 95 218 68 HOH HOH A . F 6 HOH 96 219 69 HOH HOH A . F 6 HOH 97 220 70 HOH HOH A . F 6 HOH 98 221 71 HOH HOH A . F 6 HOH 99 222 72 HOH HOH A . F 6 HOH 100 223 73 HOH HOH A . F 6 HOH 101 224 74 HOH HOH A . F 6 HOH 102 225 75 HOH HOH A . F 6 HOH 103 226 76 HOH HOH A . F 6 HOH 104 227 77 HOH HOH A . F 6 HOH 105 228 78 HOH HOH A . F 6 HOH 106 229 79 HOH HOH A . F 6 HOH 107 230 80 HOH HOH A . F 6 HOH 108 231 81 HOH HOH A . F 6 HOH 109 232 82 HOH HOH A . F 6 HOH 110 233 83 HOH HOH A . F 6 HOH 111 234 84 HOH HOH A . F 6 HOH 112 235 85 HOH HOH A . F 6 HOH 113 236 86 HOH HOH A . F 6 HOH 114 237 87 HOH HOH A . F 6 HOH 115 238 88 HOH HOH A . F 6 HOH 116 239 89 HOH HOH A . F 6 HOH 117 240 90 HOH HOH A . F 6 HOH 118 241 91 HOH HOH A . F 6 HOH 119 242 92 HOH HOH A . F 6 HOH 120 243 93 HOH HOH A . F 6 HOH 121 244 94 HOH HOH A . F 6 HOH 122 245 95 HOH HOH A . F 6 HOH 123 246 96 HOH HOH A . F 6 HOH 124 247 97 HOH HOH A . F 6 HOH 125 248 98 HOH HOH A . F 6 HOH 126 249 99 HOH HOH A . F 6 HOH 127 250 100 HOH HOH A . F 6 HOH 128 251 101 HOH HOH A . F 6 HOH 129 252 102 HOH HOH A . F 6 HOH 130 253 103 HOH HOH A . F 6 HOH 131 254 104 HOH HOH A . F 6 HOH 132 255 105 HOH HOH A . F 6 HOH 133 256 106 HOH HOH A . F 6 HOH 134 257 107 HOH HOH A . F 6 HOH 135 258 108 HOH HOH A . F 6 HOH 136 259 109 HOH HOH A . F 6 HOH 137 260 110 HOH HOH A . F 6 HOH 138 261 111 HOH HOH A . F 6 HOH 139 262 112 HOH HOH A . F 6 HOH 140 263 113 HOH HOH A . F 6 HOH 141 264 114 HOH HOH A . F 6 HOH 142 265 115 HOH HOH A . F 6 HOH 143 266 116 HOH HOH A . F 6 HOH 144 267 117 HOH HOH A . F 6 HOH 145 268 118 HOH HOH A . F 6 HOH 146 269 119 HOH HOH A . F 6 HOH 147 270 120 HOH HOH A . F 6 HOH 148 271 121 HOH HOH A . F 6 HOH 149 272 122 HOH HOH A . F 6 HOH 150 273 123 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 31 A MSE 30 ? MET SELENOMETHIONINE 3 A MSE 35 A MSE 34 ? MET SELENOMETHIONINE 4 A MSE 88 A MSE 87 ? 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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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)' 3740 ? 1 MORE -15 ? 1 'SSA (A^2)' 11370 ? # 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' 7_556 y,x,-z+1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 67.3390000000 # 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 2010-04-14 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' 8 5 '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 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 6 5 '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 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' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 13.3645 _pdbx_refine_tls.origin_y 14.6032 _pdbx_refine_tls.origin_z 22.1808 _pdbx_refine_tls.T[1][1] 0.0188 _pdbx_refine_tls.T[2][2] 0.0006 _pdbx_refine_tls.T[3][3] 0.0103 _pdbx_refine_tls.T[1][2] -0.0020 _pdbx_refine_tls.T[1][3] -0.0007 _pdbx_refine_tls.T[2][3] -0.0013 _pdbx_refine_tls.L[1][1] 0.6330 _pdbx_refine_tls.L[2][2] 0.2736 _pdbx_refine_tls.L[3][3] 0.5315 _pdbx_refine_tls.L[1][2] -0.1045 _pdbx_refine_tls.L[1][3] 0.1446 _pdbx_refine_tls.L[2][3] 0.0454 _pdbx_refine_tls.S[1][1] 0.0071 _pdbx_refine_tls.S[2][2] 0.0057 _pdbx_refine_tls.S[3][3] -0.0128 _pdbx_refine_tls.S[1][2] -0.0010 _pdbx_refine_tls.S[1][3] -0.0237 _pdbx_refine_tls.S[2][3] 0.0019 _pdbx_refine_tls.S[2][1] -0.0482 _pdbx_refine_tls.S[3][1] -0.0075 _pdbx_refine_tls.S[3][2] -0.0063 # 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 0 A 119 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 A 120 A 120 ? . . . . ? # _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 3LYG _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 ? # 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 LYS A 29 ? ? -95.60 48.15 2 1 MSE A 34 ? ? -175.27 132.81 3 1 ALA A 89 ? ? -170.29 135.92 4 1 ASP A 111 ? ? -69.60 95.38 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 IMIDAZOLE IMD 3 'UNKNOWN LIGAND' UNL 4 'SULFATE ION' SO4 5 GLYCEROL GOL 6 water HOH #