data_3KNY # _entry.id 3KNY # _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 3KNY pdb_00003kny 10.2210/pdb3kny/pdb RCSB RCSB056228 ? ? WWPDB D_1000056228 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 393001 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3KNY _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-11-12 _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.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 hypothetical protein BT_3535 (NP_812447.1) from BACTERIODES THETAIOTAOMICRON VPI-5482 at 2.60 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 3KNY _cell.length_a 120.029 _cell.length_b 120.029 _cell.length_c 94.767 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _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 3KNY _symmetry.Int_Tables_number 181 _symmetry.space_group_name_H-M 'P 64 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'hypothetical protein BT_3535' _entity.formula_weight 24645.857 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 ;GACEQNEDWVVNEP(MSE)QSFEENPEYAPLNTIPDWVSEKVTPKEYELWRT(MSE)SSRYEINYSFLKKDISEKRKKEI YDCINNICERIEKGQINKYEGFLNIADEDGTTLSDSQYFGRIATRSPEGGAEYKTNGCTLYTHSLGPYIKAAVTYKKSDD DVTITSSSVYTGSPYLGNDPSFSGASSVSYDKDKKLIAASCSGTLSFKDGSRKVEVTVQKTGF(MSE)IP ; _entity_poly.pdbx_seq_one_letter_code_can ;GACEQNEDWVVNEPMQSFEENPEYAPLNTIPDWVSEKVTPKEYELWRTMSSRYEINYSFLKKDISEKRKKEIYDCINNIC ERIEKGQINKYEGFLNIADEDGTTLSDSQYFGRIATRSPEGGAEYKTNGCTLYTHSLGPYIKAAVTYKKSDDDVTITSSS VYTGSPYLGNDPSFSGASSVSYDKDKKLIAASCSGTLSFKDGSRKVEVTVQKTGFMIP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 393001 # 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 ALA n 1 3 CYS n 1 4 GLU n 1 5 GLN n 1 6 ASN n 1 7 GLU n 1 8 ASP n 1 9 TRP n 1 10 VAL n 1 11 VAL n 1 12 ASN n 1 13 GLU n 1 14 PRO n 1 15 MSE n 1 16 GLN n 1 17 SER n 1 18 PHE n 1 19 GLU n 1 20 GLU n 1 21 ASN n 1 22 PRO n 1 23 GLU n 1 24 TYR n 1 25 ALA n 1 26 PRO n 1 27 LEU n 1 28 ASN n 1 29 THR n 1 30 ILE n 1 31 PRO n 1 32 ASP n 1 33 TRP n 1 34 VAL n 1 35 SER n 1 36 GLU n 1 37 LYS n 1 38 VAL n 1 39 THR n 1 40 PRO n 1 41 LYS n 1 42 GLU n 1 43 TYR n 1 44 GLU n 1 45 LEU n 1 46 TRP n 1 47 ARG n 1 48 THR n 1 49 MSE n 1 50 SER n 1 51 SER n 1 52 ARG n 1 53 TYR n 1 54 GLU n 1 55 ILE n 1 56 ASN n 1 57 TYR n 1 58 SER n 1 59 PHE n 1 60 LEU n 1 61 LYS n 1 62 LYS n 1 63 ASP n 1 64 ILE n 1 65 SER n 1 66 GLU n 1 67 LYS n 1 68 ARG n 1 69 LYS n 1 70 LYS n 1 71 GLU n 1 72 ILE n 1 73 TYR n 1 74 ASP n 1 75 CYS n 1 76 ILE n 1 77 ASN n 1 78 ASN n 1 79 ILE n 1 80 CYS n 1 81 GLU n 1 82 ARG n 1 83 ILE n 1 84 GLU n 1 85 LYS n 1 86 GLY n 1 87 GLN n 1 88 ILE n 1 89 ASN n 1 90 LYS n 1 91 TYR n 1 92 GLU n 1 93 GLY n 1 94 PHE n 1 95 LEU n 1 96 ASN n 1 97 ILE n 1 98 ALA n 1 99 ASP n 1 100 GLU n 1 101 ASP n 1 102 GLY n 1 103 THR n 1 104 THR n 1 105 LEU n 1 106 SER n 1 107 ASP n 1 108 SER n 1 109 GLN n 1 110 TYR n 1 111 PHE n 1 112 GLY n 1 113 ARG n 1 114 ILE n 1 115 ALA n 1 116 THR n 1 117 ARG n 1 118 SER n 1 119 PRO n 1 120 GLU n 1 121 GLY n 1 122 GLY n 1 123 ALA n 1 124 GLU n 1 125 TYR n 1 126 LYS n 1 127 THR n 1 128 ASN n 1 129 GLY n 1 130 CYS n 1 131 THR n 1 132 LEU n 1 133 TYR n 1 134 THR n 1 135 HIS n 1 136 SER n 1 137 LEU n 1 138 GLY n 1 139 PRO n 1 140 TYR n 1 141 ILE n 1 142 LYS n 1 143 ALA n 1 144 ALA n 1 145 VAL n 1 146 THR n 1 147 TYR n 1 148 LYS n 1 149 LYS n 1 150 SER n 1 151 ASP n 1 152 ASP n 1 153 ASP n 1 154 VAL n 1 155 THR n 1 156 ILE n 1 157 THR n 1 158 SER n 1 159 SER n 1 160 SER n 1 161 VAL n 1 162 TYR n 1 163 THR n 1 164 GLY n 1 165 SER n 1 166 PRO n 1 167 TYR n 1 168 LEU n 1 169 GLY n 1 170 ASN n 1 171 ASP n 1 172 PRO n 1 173 SER n 1 174 PHE n 1 175 SER n 1 176 GLY n 1 177 ALA n 1 178 SER n 1 179 SER n 1 180 VAL n 1 181 SER n 1 182 TYR n 1 183 ASP n 1 184 LYS n 1 185 ASP n 1 186 LYS n 1 187 LYS n 1 188 LEU n 1 189 ILE n 1 190 ALA n 1 191 ALA n 1 192 SER n 1 193 CYS n 1 194 SER n 1 195 GLY n 1 196 THR n 1 197 LEU n 1 198 SER n 1 199 PHE n 1 200 LYS n 1 201 ASP n 1 202 GLY n 1 203 SER n 1 204 ARG n 1 205 LYS n 1 206 VAL n 1 207 GLU n 1 208 VAL n 1 209 THR n 1 210 VAL n 1 211 GLN n 1 212 LYS n 1 213 THR n 1 214 GLY n 1 215 PHE n 1 216 MSE n 1 217 ILE n 1 218 PRO 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 BT_3535 _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 'Bacteroides thetaiotaomicron VPI-5482' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 226186 _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 Q8A1X3_BACTN _struct_ref.pdbx_db_accession Q8A1X3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ACEQNEDWVVNEPMQSFEENPEYAPLNTIPDWVSEKVTPKEYELWRTMSSRYEINYSFLKKDISEKRKKEIYDCINNICE RIEKGQINKYEGFLNIADEDGTTLSDSQYFGRIATRSPEGGAEYKTNGCTLYTHSLGPYIKAAVTYKKSDDDVTITSSSV YTGSPYLGNDPSFSGASSVSYDKDKKLIAASCSGTLSFKDGSRKVEVTVQKTGFMIP ; _struct_ref.pdbx_align_begin 18 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3KNY _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 218 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8A1X3 _struct_ref_seq.db_align_beg 18 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 234 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 18 _struct_ref_seq.pdbx_auth_seq_align_end 234 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3KNY _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 Q8A1X3 _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 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 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 3KNY # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 4.00 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 69.23 _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 6.93 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '40.9000% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 6.93, 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 2009-07-08 # _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 0.91162 1.0 2 0.97941 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 0.91162,0.97941 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3KNY _reflns.d_resolution_high 2.60 _reflns.d_resolution_low 28.831 _reflns.number_obs 12900 _reflns.pdbx_Rmerge_I_obs 0.124 _reflns.pdbx_netI_over_sigmaI 16.700 _reflns.pdbx_Rsym_value 0.124 _reflns.pdbx_redundancy 10.500 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.60 2.67 ? 10029 ? 0.011 0.7 1.056 ? 10.70 ? 941 100.00 1 1 2.67 2.74 ? 9701 ? 0.011 0.9 0.822 ? 10.80 ? 902 100.00 2 1 2.74 2.82 ? 9399 ? 0.011 1.1 0.692 ? 10.80 ? 870 100.00 3 1 2.82 2.91 ? 9369 ? 0.011 1.4 0.564 ? 10.80 ? 866 100.00 4 1 2.91 3.00 ? 9033 ? 0.011 1.8 0.440 ? 10.70 ? 842 100.00 5 1 3.00 3.11 ? 8566 ? 0.011 2.4 0.326 ? 10.80 ? 790 100.00 6 1 3.11 3.22 ? 8399 ? 0.011 3.0 0.259 ? 10.70 ? 784 100.00 7 1 3.22 3.36 ? 8120 ? 0.011 3.8 0.199 ? 10.60 ? 763 100.00 8 1 3.36 3.51 ? 7630 ? 0.011 4.7 0.154 ? 10.70 ? 715 100.00 9 1 3.51 3.68 ? 7463 ? 0.011 5.8 0.125 ? 10.70 ? 700 100.00 10 1 3.68 3.88 ? 7087 ? 0.011 6.7 0.109 ? 10.50 ? 672 100.00 11 1 3.88 4.11 ? 6580 ? 0.011 7.7 0.094 ? 10.60 ? 621 100.00 12 1 4.11 4.39 ? 6332 ? 0.011 9.1 0.074 ? 10.50 ? 604 100.00 13 1 4.39 4.75 ? 5902 ? 0.011 10.8 0.063 ? 10.40 ? 567 100.00 14 1 4.75 5.20 ? 5322 ? 0.011 10.8 0.061 ? 10.40 ? 513 100.00 15 1 5.20 5.81 ? 4904 ? 0.011 9.6 0.070 ? 10.30 ? 478 100.00 16 1 5.81 6.71 ? 4280 ? 0.011 9.2 0.073 ? 10.00 ? 429 100.00 17 1 6.71 8.22 ? 3576 ? 0.011 10.1 0.063 ? 9.80 ? 364 100.00 18 1 8.22 11.63 ? 2841 ? 0.011 10.9 0.053 ? 9.30 ? 304 100.00 19 1 11.63 28.83 ? 1398 ? 0.011 12.4 0.048 ? 8.00 ? 175 93.80 20 1 # _refine.entry_id 3KNY _refine.ls_d_res_high 2.600 _refine.ls_d_res_low 28.831 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.870 _refine.ls_number_reflns_obs 12878 _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 0.204 _refine.ls_R_factor_R_work 0.202 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.239 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 629 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 39.252 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.280 _refine.aniso_B[2][2] 1.280 _refine.aniso_B[3][3] -1.920 _refine.aniso_B[1][2] 0.640 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.946 _refine.correlation_coeff_Fo_to_Fc_free 0.922 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.269 _refine.pdbx_overall_ESU_R_Free 0.224 _refine.overall_SU_ML 0.171 _refine.overall_SU_B 18.125 _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 86.95 _refine.B_iso_min 10.55 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _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 1526 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1526 _refine_hist.d_res_high 2.600 _refine_hist.d_res_low 28.831 # 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' 1573 0.015 0.022 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 1068 0.002 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 2132 1.536 1.959 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 2620 0.819 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 194 5.773 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 68 33.512 25.294 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 274 16.351 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 4 11.566 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 231 0.084 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 1736 0.006 0.021 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 304 0.001 0.020 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 970 1.675 3.000 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 390 0.313 3.000 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 1575 3.187 5.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 603 5.109 8.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 556 7.184 11.000 ? ? # _refine_ls_shell.d_res_high 2.600 _refine_ls_shell.d_res_low 2.667 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.790 _refine_ls_shell.number_reflns_R_work 894 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.361 _refine_ls_shell.R_factor_R_free 0.407 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 45 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 939 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3KNY _struct.title ;Crystal structure of a two domain protein with unknown function (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 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 3KNY # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details 'ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.' # 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 SER A 17 ? ASN A 21 ? SER A 33 ASN A 37 5 ? 5 HELX_P HELX_P2 2 PRO A 31 ? LYS A 37 ? PRO A 47 LYS A 53 5 ? 7 HELX_P HELX_P3 3 THR A 39 ? SER A 50 ? THR A 55 SER A 66 1 ? 12 HELX_P HELX_P4 4 TYR A 57 ? LYS A 61 ? TYR A 73 LYS A 77 5 ? 5 HELX_P HELX_P5 5 SER A 65 ? LYS A 85 ? SER A 81 LYS A 101 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 MSE 15 C ? ? ? 1_555 A GLN 16 N ? ? A MSE 31 A GLN 32 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale2 covale both ? A MSE 49 C ? ? ? 1_555 A SER 50 N ? ? A MSE 65 A SER 66 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale3 covale both ? A MSE 216 C ? ? ? 1_555 A ILE 217 N ? ? A MSE 232 A ILE 233 1_555 ? ? ? ? ? ? ? 1.336 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? C ? 3 ? # 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 ? anti-parallel B 3 4 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? 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 GLU A 7 ? VAL A 10 ? GLU A 23 VAL A 26 A 2 ARG A 204 ? ILE A 217 ? ARG A 220 ILE A 233 A 3 GLY A 93 ? ILE A 97 ? GLY A 109 ILE A 113 A 4 TYR A 53 ? ILE A 55 ? TYR A 69 ILE A 71 B 1 GLU A 7 ? VAL A 10 ? GLU A 23 VAL A 26 B 2 ARG A 204 ? ILE A 217 ? ARG A 220 ILE A 233 B 3 LEU A 188 ? ASP A 201 ? LEU A 204 ASP A 217 B 4 SER A 173 ? ASP A 183 ? SER A 189 ASP A 199 C 1 GLU A 124 ? THR A 134 ? GLU A 140 THR A 150 C 2 TYR A 140 ? LYS A 149 ? TYR A 156 LYS A 165 C 3 VAL A 154 ? GLY A 164 ? VAL A 170 GLY A 180 # 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 VAL A 10 ? N VAL A 26 O THR A 209 ? O THR A 225 A 2 3 O ILE A 217 ? O ILE A 233 N ASN A 96 ? N ASN A 112 A 3 4 O GLY A 93 ? O GLY A 109 N GLU A 54 ? N GLU A 70 B 1 2 N VAL A 10 ? N VAL A 26 O THR A 209 ? O THR A 225 B 2 3 O VAL A 208 ? O VAL A 224 N LEU A 197 ? N LEU A 213 B 3 4 O LEU A 188 ? O LEU A 204 N ASP A 183 ? N ASP A 199 C 1 2 N CYS A 130 ? N CYS A 146 O ALA A 143 ? O ALA A 159 C 2 3 N LYS A 142 ? N LYS A 158 O TYR A 162 ? O TYR A 178 # _atom_sites.entry_id 3KNY _atom_sites.fract_transf_matrix[1][1] 0.008331 _atom_sites.fract_transf_matrix[1][2] 0.004810 _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] 0.009620 _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] 0.010552 _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 ALA 2 18 ? ? ? A . n A 1 3 CYS 3 19 ? ? ? A . n A 1 4 GLU 4 20 ? ? ? A . n A 1 5 GLN 5 21 ? ? ? A . n A 1 6 ASN 6 22 22 ASN ASN A . n A 1 7 GLU 7 23 23 GLU GLU A . n A 1 8 ASP 8 24 24 ASP ASP A . n A 1 9 TRP 9 25 25 TRP TRP A . n A 1 10 VAL 10 26 26 VAL VAL A . n A 1 11 VAL 11 27 27 VAL VAL A . n A 1 12 ASN 12 28 28 ASN ASN A . n A 1 13 GLU 13 29 29 GLU GLU A . n A 1 14 PRO 14 30 30 PRO PRO A . n A 1 15 MSE 15 31 31 MSE MSE A . n A 1 16 GLN 16 32 32 GLN GLN A . n A 1 17 SER 17 33 33 SER SER A . n A 1 18 PHE 18 34 34 PHE PHE A . n A 1 19 GLU 19 35 35 GLU GLU A . n A 1 20 GLU 20 36 36 GLU GLU A . n A 1 21 ASN 21 37 37 ASN ASN A . n A 1 22 PRO 22 38 38 PRO PRO A . n A 1 23 GLU 23 39 39 GLU GLU A . n A 1 24 TYR 24 40 40 TYR TYR A . n A 1 25 ALA 25 41 41 ALA ALA A . n A 1 26 PRO 26 42 42 PRO PRO A . n A 1 27 LEU 27 43 43 LEU LEU A . n A 1 28 ASN 28 44 44 ASN ASN A . n A 1 29 THR 29 45 45 THR THR A . n A 1 30 ILE 30 46 46 ILE ILE A . n A 1 31 PRO 31 47 47 PRO PRO A . n A 1 32 ASP 32 48 48 ASP ASP A . n A 1 33 TRP 33 49 49 TRP TRP A . n A 1 34 VAL 34 50 50 VAL VAL A . n A 1 35 SER 35 51 51 SER SER A . n A 1 36 GLU 36 52 52 GLU GLU A . n A 1 37 LYS 37 53 53 LYS LYS A . n A 1 38 VAL 38 54 54 VAL VAL A . n A 1 39 THR 39 55 55 THR THR A . n A 1 40 PRO 40 56 56 PRO PRO A . n A 1 41 LYS 41 57 57 LYS LYS A . n A 1 42 GLU 42 58 58 GLU GLU A . n A 1 43 TYR 43 59 59 TYR TYR A . n A 1 44 GLU 44 60 60 GLU GLU A . n A 1 45 LEU 45 61 61 LEU LEU A . n A 1 46 TRP 46 62 62 TRP TRP A . n A 1 47 ARG 47 63 63 ARG ARG A . n A 1 48 THR 48 64 64 THR THR A . n A 1 49 MSE 49 65 65 MSE MSE A . n A 1 50 SER 50 66 66 SER SER A . n A 1 51 SER 51 67 67 SER SER A . n A 1 52 ARG 52 68 68 ARG ARG A . n A 1 53 TYR 53 69 69 TYR TYR A . n A 1 54 GLU 54 70 70 GLU GLU A . n A 1 55 ILE 55 71 71 ILE ILE A . n A 1 56 ASN 56 72 72 ASN ASN A . n A 1 57 TYR 57 73 73 TYR TYR A . n A 1 58 SER 58 74 74 SER SER A . n A 1 59 PHE 59 75 75 PHE PHE A . n A 1 60 LEU 60 76 76 LEU LEU A . n A 1 61 LYS 61 77 77 LYS LYS A . n A 1 62 LYS 62 78 78 LYS LYS A . n A 1 63 ASP 63 79 79 ASP ASP A . n A 1 64 ILE 64 80 80 ILE ILE A . n A 1 65 SER 65 81 81 SER SER A . n A 1 66 GLU 66 82 82 GLU GLU A . n A 1 67 LYS 67 83 83 LYS LYS A . n A 1 68 ARG 68 84 84 ARG ARG A . n A 1 69 LYS 69 85 85 LYS LYS A . n A 1 70 LYS 70 86 86 LYS LYS A . n A 1 71 GLU 71 87 87 GLU GLU A . n A 1 72 ILE 72 88 88 ILE ILE A . n A 1 73 TYR 73 89 89 TYR TYR A . n A 1 74 ASP 74 90 90 ASP ASP A . n A 1 75 CYS 75 91 91 CYS CYS A . n A 1 76 ILE 76 92 92 ILE ILE A . n A 1 77 ASN 77 93 93 ASN ASN A . n A 1 78 ASN 78 94 94 ASN ASN A . n A 1 79 ILE 79 95 95 ILE ILE A . n A 1 80 CYS 80 96 96 CYS CYS A . n A 1 81 GLU 81 97 97 GLU GLU A . n A 1 82 ARG 82 98 98 ARG ARG A . n A 1 83 ILE 83 99 99 ILE ILE A . n A 1 84 GLU 84 100 100 GLU GLU A . n A 1 85 LYS 85 101 101 LYS LYS A . n A 1 86 GLY 86 102 102 GLY GLY A . n A 1 87 GLN 87 103 103 GLN GLN A . n A 1 88 ILE 88 104 104 ILE ILE A . n A 1 89 ASN 89 105 105 ASN ASN A . n A 1 90 LYS 90 106 106 LYS LYS A . n A 1 91 TYR 91 107 107 TYR TYR A . n A 1 92 GLU 92 108 108 GLU GLU A . n A 1 93 GLY 93 109 109 GLY GLY A . n A 1 94 PHE 94 110 110 PHE PHE A . n A 1 95 LEU 95 111 111 LEU LEU A . n A 1 96 ASN 96 112 112 ASN ASN A . n A 1 97 ILE 97 113 113 ILE ILE A . n A 1 98 ALA 98 114 114 ALA ALA A . n A 1 99 ASP 99 115 115 ASP ASP A . n A 1 100 GLU 100 116 116 GLU GLU A . n A 1 101 ASP 101 117 117 ASP ASP A . n A 1 102 GLY 102 118 118 GLY GLY A . n A 1 103 THR 103 119 119 THR THR A . n A 1 104 THR 104 120 ? ? ? A . n A 1 105 LEU 105 121 ? ? ? A . n A 1 106 SER 106 122 ? ? ? A . n A 1 107 ASP 107 123 ? ? ? A . n A 1 108 SER 108 124 ? ? ? A . n A 1 109 GLN 109 125 ? ? ? A . n A 1 110 TYR 110 126 ? ? ? A . n A 1 111 PHE 111 127 ? ? ? A . n A 1 112 GLY 112 128 ? ? ? A . n A 1 113 ARG 113 129 ? ? ? A . n A 1 114 ILE 114 130 ? ? ? A . n A 1 115 ALA 115 131 ? ? ? A . n A 1 116 THR 116 132 ? ? ? A . n A 1 117 ARG 117 133 ? ? ? A . n A 1 118 SER 118 134 ? ? ? A . n A 1 119 PRO 119 135 ? ? ? A . n A 1 120 GLU 120 136 ? ? ? A . n A 1 121 GLY 121 137 ? ? ? A . n A 1 122 GLY 122 138 ? ? ? A . n A 1 123 ALA 123 139 139 ALA ALA A . n A 1 124 GLU 124 140 140 GLU GLU A . n A 1 125 TYR 125 141 141 TYR TYR A . n A 1 126 LYS 126 142 142 LYS LYS A . n A 1 127 THR 127 143 143 THR THR A . n A 1 128 ASN 128 144 144 ASN ASN A . n A 1 129 GLY 129 145 145 GLY GLY A . n A 1 130 CYS 130 146 146 CYS CYS A . n A 1 131 THR 131 147 147 THR THR A . n A 1 132 LEU 132 148 148 LEU LEU A . n A 1 133 TYR 133 149 149 TYR TYR A . n A 1 134 THR 134 150 150 THR THR A . n A 1 135 HIS 135 151 151 HIS HIS A . n A 1 136 SER 136 152 152 SER SER A . n A 1 137 LEU 137 153 153 LEU LEU A . n A 1 138 GLY 138 154 154 GLY GLY A . n A 1 139 PRO 139 155 155 PRO PRO A . n A 1 140 TYR 140 156 156 TYR TYR A . n A 1 141 ILE 141 157 157 ILE ILE A . n A 1 142 LYS 142 158 158 LYS LYS A . n A 1 143 ALA 143 159 159 ALA ALA A . n A 1 144 ALA 144 160 160 ALA ALA A . n A 1 145 VAL 145 161 161 VAL VAL A . n A 1 146 THR 146 162 162 THR THR A . n A 1 147 TYR 147 163 163 TYR TYR A . n A 1 148 LYS 148 164 164 LYS LYS A . n A 1 149 LYS 149 165 165 LYS LYS A . n A 1 150 SER 150 166 166 SER SER A . n A 1 151 ASP 151 167 167 ASP ASP A . n A 1 152 ASP 152 168 168 ASP ASP A . n A 1 153 ASP 153 169 169 ASP ASP A . n A 1 154 VAL 154 170 170 VAL VAL A . n A 1 155 THR 155 171 171 THR THR A . n A 1 156 ILE 156 172 172 ILE ILE A . n A 1 157 THR 157 173 173 THR THR A . n A 1 158 SER 158 174 174 SER SER A . n A 1 159 SER 159 175 175 SER SER A . n A 1 160 SER 160 176 176 SER SER A . n A 1 161 VAL 161 177 177 VAL VAL A . n A 1 162 TYR 162 178 178 TYR TYR A . n A 1 163 THR 163 179 179 THR THR A . n A 1 164 GLY 164 180 180 GLY GLY A . n A 1 165 SER 165 181 181 SER SER A . n A 1 166 PRO 166 182 182 PRO PRO A . n A 1 167 TYR 167 183 183 TYR TYR A . n A 1 168 LEU 168 184 184 LEU LEU A . n A 1 169 GLY 169 185 185 GLY GLY A . n A 1 170 ASN 170 186 186 ASN ASN A . n A 1 171 ASP 171 187 187 ASP ASP A . n A 1 172 PRO 172 188 188 PRO PRO A . n A 1 173 SER 173 189 189 SER SER A . n A 1 174 PHE 174 190 190 PHE PHE A . n A 1 175 SER 175 191 191 SER SER A . n A 1 176 GLY 176 192 192 GLY GLY A . n A 1 177 ALA 177 193 193 ALA ALA A . n A 1 178 SER 178 194 194 SER SER A . n A 1 179 SER 179 195 195 SER SER A . n A 1 180 VAL 180 196 196 VAL VAL A . n A 1 181 SER 181 197 197 SER SER A . n A 1 182 TYR 182 198 198 TYR TYR A . n A 1 183 ASP 183 199 199 ASP ASP A . n A 1 184 LYS 184 200 200 LYS LYS A . n A 1 185 ASP 185 201 201 ASP ASP A . n A 1 186 LYS 186 202 202 LYS LYS A . n A 1 187 LYS 187 203 203 LYS LYS A . n A 1 188 LEU 188 204 204 LEU LEU A . n A 1 189 ILE 189 205 205 ILE ILE A . n A 1 190 ALA 190 206 206 ALA ALA A . n A 1 191 ALA 191 207 207 ALA ALA A . n A 1 192 SER 192 208 208 SER SER A . n A 1 193 CYS 193 209 209 CYS CYS A . n A 1 194 SER 194 210 210 SER SER A . n A 1 195 GLY 195 211 211 GLY GLY A . n A 1 196 THR 196 212 212 THR THR A . n A 1 197 LEU 197 213 213 LEU LEU A . n A 1 198 SER 198 214 214 SER SER A . n A 1 199 PHE 199 215 215 PHE PHE A . n A 1 200 LYS 200 216 216 LYS LYS A . n A 1 201 ASP 201 217 217 ASP ASP A . n A 1 202 GLY 202 218 218 GLY GLY A . n A 1 203 SER 203 219 219 SER SER A . n A 1 204 ARG 204 220 220 ARG ARG A . n A 1 205 LYS 205 221 221 LYS LYS A . n A 1 206 VAL 206 222 222 VAL VAL A . n A 1 207 GLU 207 223 223 GLU GLU A . n A 1 208 VAL 208 224 224 VAL VAL A . n A 1 209 THR 209 225 225 THR THR A . n A 1 210 VAL 210 226 226 VAL VAL A . n A 1 211 GLN 211 227 227 GLN GLN A . n A 1 212 LYS 212 228 228 LYS LYS A . n A 1 213 THR 213 229 229 THR THR A . n A 1 214 GLY 214 230 230 GLY GLY A . n A 1 215 PHE 215 231 231 PHE PHE A . n A 1 216 MSE 216 232 232 MSE MSE A . n A 1 217 ILE 217 233 233 ILE ILE A . n A 1 218 PRO 218 234 234 PRO PRO 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_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 15 A MSE 31 ? MET SELENOMETHIONINE 2 A MSE 49 A MSE 65 ? MET SELENOMETHIONINE 3 A MSE 216 A MSE 232 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A 2 1,2 A # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 1410 ? 2 MORE 0 ? 2 'SSA (A^2)' 18790 ? # 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' 9_764 -x+2,-x+y+1,-z-1/3 -0.5000000000 -0.8660254038 0.0000000000 180.0435000000 -0.8660254038 0.5000000000 0.0000000000 103.9481631908 0.0000000000 0.0000000000 -1.0000000000 -31.5890000000 # 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 2009-12-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 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' 'Author supporting evidence' 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' 8 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' pdbx_struct_assembly_auth_evidence 2 3 'Structure model' software 3 4 'Structure model' software 4 4 'Structure model' struct_conn 5 5 'Structure model' database_2 6 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' # _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 87.2446 _pdbx_refine_tls.origin_y 32.9840 _pdbx_refine_tls.origin_z -4.0255 _pdbx_refine_tls.T[1][1] 0.1326 _pdbx_refine_tls.T[2][2] 0.0877 _pdbx_refine_tls.T[3][3] 0.0905 _pdbx_refine_tls.T[1][2] -0.0389 _pdbx_refine_tls.T[1][3] 0.0216 _pdbx_refine_tls.T[2][3] 0.0683 _pdbx_refine_tls.L[1][1] 2.1646 _pdbx_refine_tls.L[2][2] 2.1458 _pdbx_refine_tls.L[3][3] 2.5958 _pdbx_refine_tls.L[1][2] -0.0790 _pdbx_refine_tls.L[1][3] 0.0565 _pdbx_refine_tls.L[2][3] -0.5020 _pdbx_refine_tls.S[1][1] 0.0022 _pdbx_refine_tls.S[2][2] -0.0696 _pdbx_refine_tls.S[3][3] 0.0674 _pdbx_refine_tls.S[1][2] -0.3427 _pdbx_refine_tls.S[1][3] -0.4283 _pdbx_refine_tls.S[2][3] 0.0818 _pdbx_refine_tls.S[2][1] 0.3511 _pdbx_refine_tls.S[3][1] 0.2689 _pdbx_refine_tls.S[3][2] 0.0283 # _pdbx_refine_tls_group.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_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 22 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 234 _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 ? # _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 5.5.0053 ? 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 3.2.5 5/04/2004 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 3KNY _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT (RESIDUES 18-234) 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_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 NE _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 ARG _pdbx_validate_symm_contact.auth_seq_id_1 220 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 NE _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 ARG _pdbx_validate_symm_contact.auth_seq_id_2 220 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 10_664 _pdbx_validate_symm_contact.dist 2.11 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 CYS _pdbx_validate_rmsd_bond.auth_seq_id_1 146 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 SG _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 CYS _pdbx_validate_rmsd_bond.auth_seq_id_2 146 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.579 _pdbx_validate_rmsd_bond.bond_target_value 1.812 _pdbx_validate_rmsd_bond.bond_deviation -0.233 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.016 _pdbx_validate_rmsd_bond.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 SER A 51 ? ? -59.81 -8.22 2 1 LYS A 77 ? ? -89.64 36.66 3 1 ILE A 104 ? ? -106.23 79.44 4 1 ASP A 117 ? ? -39.23 121.22 5 1 CYS A 146 ? ? -171.94 127.29 6 1 ASP A 217 ? ? -112.37 70.25 # 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 ASN 22 ? CG ? A ASN 6 CG 2 1 Y 1 A ASN 22 ? OD1 ? A ASN 6 OD1 3 1 Y 1 A ASN 22 ? ND2 ? A ASN 6 ND2 4 1 Y 1 A GLU 23 ? CG ? A GLU 7 CG 5 1 Y 1 A GLU 23 ? CD ? A GLU 7 CD 6 1 Y 1 A GLU 23 ? OE1 ? A GLU 7 OE1 7 1 Y 1 A GLU 23 ? OE2 ? A GLU 7 OE2 8 1 Y 1 A GLU 35 ? CD ? A GLU 19 CD 9 1 Y 1 A GLU 35 ? OE1 ? A GLU 19 OE1 10 1 Y 1 A GLU 35 ? OE2 ? A GLU 19 OE2 11 1 Y 1 A ASP 167 ? CG ? A ASP 151 CG 12 1 Y 1 A ASP 167 ? OD1 ? A ASP 151 OD1 13 1 Y 1 A ASP 167 ? OD2 ? A ASP 151 OD2 14 1 Y 1 A ARG 220 ? CZ ? A ARG 204 CZ 15 1 Y 1 A ARG 220 ? NH1 ? A ARG 204 NH1 16 1 Y 1 A ARG 220 ? NH2 ? A ARG 204 NH2 17 1 Y 1 A LYS 221 ? CD ? A LYS 205 CD 18 1 Y 1 A LYS 221 ? CE ? A LYS 205 CE 19 1 Y 1 A LYS 221 ? NZ ? A LYS 205 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 GLY 0 ? A GLY 1 2 1 Y 1 A ALA 18 ? A ALA 2 3 1 Y 1 A CYS 19 ? A CYS 3 4 1 Y 1 A GLU 20 ? A GLU 4 5 1 Y 1 A GLN 21 ? A GLN 5 6 1 Y 1 A THR 120 ? A THR 104 7 1 Y 1 A LEU 121 ? A LEU 105 8 1 Y 1 A SER 122 ? A SER 106 9 1 Y 1 A ASP 123 ? A ASP 107 10 1 Y 1 A SER 124 ? A SER 108 11 1 Y 1 A GLN 125 ? A GLN 109 12 1 Y 1 A TYR 126 ? A TYR 110 13 1 Y 1 A PHE 127 ? A PHE 111 14 1 Y 1 A GLY 128 ? A GLY 112 15 1 Y 1 A ARG 129 ? A ARG 113 16 1 Y 1 A ILE 130 ? A ILE 114 17 1 Y 1 A ALA 131 ? A ALA 115 18 1 Y 1 A THR 132 ? A THR 116 19 1 Y 1 A ARG 133 ? A ARG 117 20 1 Y 1 A SER 134 ? A SER 118 21 1 Y 1 A PRO 135 ? A PRO 119 22 1 Y 1 A GLU 136 ? A GLU 120 23 1 Y 1 A GLY 137 ? A GLY 121 24 1 Y 1 A GLY 138 ? A GLY 122 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #