data_3EBR # _entry.id 3EBR # _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 3EBR pdb_00003ebr 10.2210/pdb3ebr/pdb RCSB RCSB049125 ? ? WWPDB D_1000049125 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 371684 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3EBR _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-08-28 _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 RmlC-like cupin with unknown function (YP_294607.1) from RALSTONIA EUTROPHA JMP134 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 3EBR _cell.length_a 91.157 _cell.length_b 91.157 _cell.length_c 48.753 _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 3EBR _symmetry.Int_Tables_number 93 _symmetry.space_group_name_H-M 'P 42 2 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 'uncharacterized RmlC-like cupin' 18260.641 1 ? ? ? ? 2 non-polymer syn 'DI(HYDROXYETHYL)ETHER' 106.120 4 ? ? ? ? 3 water nat water 18.015 25 ? ? ? ? # _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)LFESINTGCLDGNDTPW(MSE)PFAPYSNDV(MSE)VKYFKIDPVRGETITLLKAPAG(MSE)E(MSE)PRHHH TGTVIVYTVQGSWRYKEHDWVAHAGSVVYETASTRHTPQSAYAEGPDIITFNIVAGELLYLDDKDNIIAVENWKTS (MSE)DRYLNYCKAHGIRPKDLSTFEG ; _entity_poly.pdbx_seq_one_letter_code_can ;GMLFESINTGCLDGNDTPWMPFAPYSNDVMVKYFKIDPVRGETITLLKAPAGMEMPRHHHTGTVIVYTVQGSWRYKEHDW VAHAGSVVYETASTRHTPQSAYAEGPDIITFNIVAGELLYLDDKDNIIAVENWKTSMDRYLNYCKAHGIRPKDLSTFEG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 371684 # 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 LEU n 1 4 PHE n 1 5 GLU n 1 6 SER n 1 7 ILE n 1 8 ASN n 1 9 THR n 1 10 GLY n 1 11 CYS n 1 12 LEU n 1 13 ASP n 1 14 GLY n 1 15 ASN n 1 16 ASP n 1 17 THR n 1 18 PRO n 1 19 TRP n 1 20 MSE n 1 21 PRO n 1 22 PHE n 1 23 ALA n 1 24 PRO n 1 25 TYR n 1 26 SER n 1 27 ASN n 1 28 ASP n 1 29 VAL n 1 30 MSE n 1 31 VAL n 1 32 LYS n 1 33 TYR n 1 34 PHE n 1 35 LYS n 1 36 ILE n 1 37 ASP n 1 38 PRO n 1 39 VAL n 1 40 ARG n 1 41 GLY n 1 42 GLU n 1 43 THR n 1 44 ILE n 1 45 THR n 1 46 LEU n 1 47 LEU n 1 48 LYS n 1 49 ALA n 1 50 PRO n 1 51 ALA n 1 52 GLY n 1 53 MSE n 1 54 GLU n 1 55 MSE n 1 56 PRO n 1 57 ARG n 1 58 HIS n 1 59 HIS n 1 60 HIS n 1 61 THR n 1 62 GLY n 1 63 THR n 1 64 VAL n 1 65 ILE n 1 66 VAL n 1 67 TYR n 1 68 THR n 1 69 VAL n 1 70 GLN n 1 71 GLY n 1 72 SER n 1 73 TRP n 1 74 ARG n 1 75 TYR n 1 76 LYS n 1 77 GLU n 1 78 HIS n 1 79 ASP n 1 80 TRP n 1 81 VAL n 1 82 ALA n 1 83 HIS n 1 84 ALA n 1 85 GLY n 1 86 SER n 1 87 VAL n 1 88 VAL n 1 89 TYR n 1 90 GLU n 1 91 THR n 1 92 ALA n 1 93 SER n 1 94 THR n 1 95 ARG n 1 96 HIS n 1 97 THR n 1 98 PRO n 1 99 GLN n 1 100 SER n 1 101 ALA n 1 102 TYR n 1 103 ALA n 1 104 GLU n 1 105 GLY n 1 106 PRO n 1 107 ASP n 1 108 ILE n 1 109 ILE n 1 110 THR n 1 111 PHE n 1 112 ASN n 1 113 ILE n 1 114 VAL n 1 115 ALA n 1 116 GLY n 1 117 GLU n 1 118 LEU n 1 119 LEU n 1 120 TYR n 1 121 LEU n 1 122 ASP n 1 123 ASP n 1 124 LYS n 1 125 ASP n 1 126 ASN n 1 127 ILE n 1 128 ILE n 1 129 ALA n 1 130 VAL n 1 131 GLU n 1 132 ASN n 1 133 TRP n 1 134 LYS n 1 135 THR n 1 136 SER n 1 137 MSE n 1 138 ASP n 1 139 ARG n 1 140 TYR n 1 141 LEU n 1 142 ASN n 1 143 TYR n 1 144 CYS n 1 145 LYS n 1 146 ALA n 1 147 HIS n 1 148 GLY n 1 149 ILE n 1 150 ARG n 1 151 PRO n 1 152 LYS n 1 153 ASP n 1 154 LEU n 1 155 SER n 1 156 THR n 1 157 PHE n 1 158 GLU n 1 159 GLY 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 'Alcaligenes eutrophus' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'YP_294607.1, Reut_A0381' _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 'Ralstonia eutropha JMP134' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 264198 _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 Q476C0_RALEJ _struct_ref.pdbx_db_accession Q476C0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MLFESINTGCLDGNDTPWMPFAPYSNDVMVKYFKIDPVRGETITLLKAPAGMEMPRHHHTGTVIVYTVQGSWRYKEHDWV AHAGSVVYETASTRHTPQSAYAEGPDIITFNIVAGELLYLDDKDNIIAVENWKTSMDRYLNYCKAHGIRPKDLSTFEG ; _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 3EBR _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 159 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q476C0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 158 _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 158 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3EBR _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 Q476C0 _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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PEG non-polymer . 'DI(HYDROXYETHYL)ETHER' ? 'C4 H10 O3' 106.120 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 3EBR # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.77 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 55.65 _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 6.5 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '60.0% polyethylene glycol 200, 0.1M HEPES pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _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 2008-06-22 # _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 0.97941 1.0 3 0.97854 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 0.91837,0.97941,0.97854 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3EBR _reflns.d_resolution_high 2.60 _reflns.d_resolution_low 28.831 _reflns.number_obs 6713 _reflns.pdbx_Rmerge_I_obs 0.074 _reflns.pdbx_netI_over_sigmaI 15.1 _reflns.pdbx_Rsym_value 0.074 _reflns.pdbx_redundancy 4.700 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate 76.248 _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 ? 2290 ? 0.596 2.2 0.596 ? 4.80 ? 476 100.0 1 1 2.67 2.74 ? 2283 ? 0.436 3.1 0.436 ? 4.90 ? 470 100.00 2 1 2.74 2.82 ? 2158 ? 0.375 3.4 0.375 ? 4.80 ? 451 100.00 3 1 2.82 2.91 ? 2176 ? 0.289 4.5 0.289 ? 4.80 ? 452 100.00 4 1 2.91 3.00 ? 2050 ? 0.203 6.2 0.203 ? 4.80 ? 430 100.00 5 1 3.00 3.11 ? 2026 ? 0.171 7.7 0.171 ? 4.80 ? 419 100.00 6 1 3.11 3.22 ? 1964 ? 0.118 10.6 0.118 ? 4.70 ? 414 100.00 7 1 3.22 3.36 ? 1844 ? 0.099 13.0 0.099 ? 4.80 ? 384 100.00 8 1 3.36 3.51 ? 1799 ? 0.079 15.7 0.079 ? 4.70 ? 383 100.00 9 1 3.51 3.68 ? 1733 ? 0.074 19.6 0.074 ? 4.80 ? 364 100.00 10 1 3.68 3.88 ? 1575 ? 0.073 21.7 0.073 ? 4.70 ? 337 100.00 11 1 3.88 4.11 ? 1571 ? 0.067 25.4 0.067 ? 4.60 ? 339 100.00 12 1 4.11 4.39 ? 1438 ? 0.058 29.5 0.058 ? 4.60 ? 310 100.00 13 1 4.39 4.75 ? 1356 ? 0.055 29.0 0.055 ? 4.60 ? 294 100.00 14 1 4.75 5.20 ? 1226 ? 0.046 30.3 0.046 ? 4.50 ? 270 100.00 15 1 5.20 5.81 ? 1122 ? 0.056 28.4 0.056 ? 4.50 ? 252 100.00 16 1 5.81 6.71 ? 989 ? 0.069 26.3 0.069 ? 4.40 ? 223 99.90 17 1 6.71 8.22 ? 831 ? 0.062 26.5 0.062 ? 4.20 ? 197 99.80 18 1 8.22 11.63 ? 643 ? 0.058 27.1 0.058 ? 4.10 ? 157 99.90 19 1 11.63 28.83 ? 318 ? 0.054 28.1 0.054 ? 3.50 ? 91 92.80 20 1 # _refine.entry_id 3EBR _refine.ls_d_res_high 2.600 _refine.ls_d_res_low 28.831 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.790 _refine.ls_number_reflns_obs 6707 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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. 4.PEG MOLECULES FROM CRYSTALLIZATION ARE MODELED INTO THIS STRUCTURE. ; _refine.ls_R_factor_obs 0.229 _refine.ls_R_factor_R_work 0.227 _refine.ls_R_factor_R_free 0.262 _refine.ls_percent_reflns_R_free 7.400 _refine.ls_number_reflns_R_free 498 _refine.B_iso_mean 48.516 _refine.aniso_B[1][1] 0.280 _refine.aniso_B[2][2] 0.280 _refine.aniso_B[3][3] -0.560 _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 0.937 _refine.correlation_coeff_Fo_to_Fc_free 0.925 _refine.pdbx_overall_ESU_R 0.669 _refine.pdbx_overall_ESU_R_Free 0.318 _refine.overall_SU_ML 0.245 _refine.overall_SU_B 24.026 _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.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.B_iso_max 84.51 _refine.B_iso_min 29.27 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _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.pdbx_isotropic_thermal_model ? _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_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 1225 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 25 _refine_hist.number_atoms_total 1278 _refine_hist.d_res_high 2.600 _refine_hist.d_res_low 28.831 # 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 1298 0.015 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 848 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1764 1.885 1.933 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2063 1.532 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 158 2.404 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 57 23.456 23.684 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 185 10.173 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 5 5.639 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 190 0.070 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1439 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 266 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 186 0.132 0.300 ? 'X-RAY DIFFRACTION' ? r_nbd_other 790 0.120 0.300 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 595 0.162 0.500 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 633 0.077 0.500 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 65 0.134 0.500 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 18 0.090 0.300 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 42 0.085 0.300 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 8 0.184 0.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 816 1.077 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 316 0.173 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1277 1.869 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 570 3.098 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 487 4.343 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.600 _refine_ls_shell.d_res_low 2.668 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 439 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.340 _refine_ls_shell.R_factor_R_free 0.512 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 37 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 476 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3EBR _struct.title 'Crystal structure of an rmlc-like cupin protein (reut_a0381) from ralstonia eutropha jmp134 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 3EBR # 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 2 ? F N N 3 ? # _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 MSE A 2 ? SER A 6 ? MSE A 1 SER A 5 5 ? 5 HELX_P HELX_P2 2 ASP A 13 ? THR A 17 ? ASP A 12 THR A 16 5 ? 5 HELX_P HELX_P3 3 ASN A 132 ? HIS A 147 ? ASN A 131 HIS A 146 1 ? 16 # _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 2 C ? ? ? 1_555 A LEU 3 N ? ? A MSE 1 A LEU 2 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale2 covale both ? A TRP 19 C ? ? ? 1_555 A MSE 20 N ? ? A TRP 18 A MSE 19 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale3 covale both ? A MSE 20 C ? ? ? 1_555 A PRO 21 N ? ? A MSE 19 A PRO 20 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale4 covale both ? A VAL 29 C ? ? ? 1_555 A MSE 30 N ? ? A VAL 28 A MSE 29 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale5 covale both ? A MSE 30 C ? ? ? 1_555 A VAL 31 N ? ? A MSE 29 A VAL 30 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale6 covale both ? A GLY 52 C ? ? ? 1_555 A MSE 53 N ? ? A GLY 51 A MSE 52 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale7 covale both ? A MSE 53 C ? ? ? 1_555 A GLU 54 N ? ? A MSE 52 A GLU 53 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale8 covale both ? A GLU 54 C ? ? ? 1_555 A MSE 55 N ? ? A GLU 53 A MSE 54 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale9 covale both ? A MSE 55 C ? ? ? 1_555 A PRO 56 N ? ? A MSE 54 A PRO 55 1_555 ? ? ? ? ? ? ? 1.363 ? ? covale10 covale both ? A SER 136 C ? ? ? 1_555 A MSE 137 N ? ? A SER 135 A MSE 136 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale11 covale both ? A MSE 137 C ? ? ? 1_555 A ASP 138 N ? ? A MSE 136 A ASP 137 1_555 ? ? ? ? ? ? ? 1.343 ? ? # _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 23 _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 22 _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 24 _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 23 _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 0.71 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? B ? 4 ? C ? 2 ? # 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 A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel C 1 2 ? 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 MSE A 20 ? PRO A 21 ? MSE A 19 PRO A 20 A 2 MSE A 30 ? ASP A 37 ? MSE A 29 ASP A 36 A 3 GLU A 42 ? ALA A 49 ? GLU A 41 ALA A 48 A 4 ILE A 108 ? ALA A 115 ? ILE A 107 ALA A 114 A 5 VAL A 64 ? GLN A 70 ? VAL A 63 GLN A 69 A 6 VAL A 87 ? GLU A 90 ? VAL A 86 GLU A 89 B 1 THR A 94 ? HIS A 96 ? THR A 93 HIS A 95 B 2 HIS A 58 ? HIS A 60 ? HIS A 57 HIS A 59 B 3 LEU A 118 ? LEU A 121 ? LEU A 117 LEU A 120 B 4 ILE A 127 ? GLU A 131 ? ILE A 126 GLU A 130 C 1 TRP A 73 ? TYR A 75 ? TRP A 72 TYR A 74 C 2 PRO A 98 ? SER A 100 ? PRO A 97 SER A 99 # 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 MSE A 20 ? N MSE A 19 O VAL A 31 ? O VAL A 30 A 2 3 N ASP A 37 ? N ASP A 36 O GLU A 42 ? O GLU A 41 A 3 4 N ALA A 49 ? N ALA A 48 O ILE A 108 ? O ILE A 107 A 4 5 O PHE A 111 ? O PHE A 110 N TYR A 67 ? N TYR A 66 A 5 6 N VAL A 66 ? N VAL A 65 O VAL A 88 ? O VAL A 87 B 1 2 O HIS A 96 ? O HIS A 95 N HIS A 58 ? N HIS A 57 B 2 3 N HIS A 59 ? N HIS A 58 O LEU A 119 ? O LEU A 118 B 3 4 N LEU A 118 ? N LEU A 117 O GLU A 131 ? O GLU A 130 C 1 2 N ARG A 74 ? N ARG A 73 O GLN A 99 ? O GLN A 98 # 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 PEG 159 ? 4 'BINDING SITE FOR RESIDUE PEG A 159' AC2 Software A PEG 160 ? 4 'BINDING SITE FOR RESIDUE PEG A 160' AC3 Software A PEG 162 ? 3 'BINDING SITE FOR RESIDUE PEG A 162' # 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 4 TYR A 25 ? TYR A 24 . ? 1_555 ? 2 AC1 4 PRO A 56 ? PRO A 55 . ? 1_555 ? 3 AC1 4 TYR A 120 ? TYR A 119 . ? 1_555 ? 4 AC1 4 HOH F . ? HOH A 183 . ? 1_555 ? 5 AC2 4 THR A 43 ? THR A 42 . ? 1_555 ? 6 AC2 4 LEU A 47 ? LEU A 46 . ? 1_555 ? 7 AC2 4 GLY A 116 ? GLY A 115 . ? 1_555 ? 8 AC2 4 HOH F . ? HOH A 165 . ? 1_555 ? 9 AC3 3 GLY A 52 ? GLY A 51 . ? 1_555 ? 10 AC3 3 ARG A 74 ? ARG A 73 . ? 1_555 ? 11 AC3 3 SER A 100 ? SER A 99 . ? 1_555 ? # _atom_sites.entry_id 3EBR _atom_sites.fract_transf_matrix[1][1] 0.010970 _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] 0.010970 _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] 0.020512 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 LEU 3 2 2 LEU LEU A . n A 1 4 PHE 4 3 3 PHE PHE A . n A 1 5 GLU 5 4 4 GLU GLU A . n A 1 6 SER 6 5 5 SER SER A . n A 1 7 ILE 7 6 6 ILE ILE A . n A 1 8 ASN 8 7 7 ASN ASN A . n A 1 9 THR 9 8 8 THR THR A . n A 1 10 GLY 10 9 9 GLY GLY A . n A 1 11 CYS 11 10 10 CYS CYS A . n A 1 12 LEU 12 11 11 LEU LEU A . n A 1 13 ASP 13 12 12 ASP ASP A . n A 1 14 GLY 14 13 13 GLY GLY A . n A 1 15 ASN 15 14 14 ASN ASN A . n A 1 16 ASP 16 15 15 ASP ASP A . n A 1 17 THR 17 16 16 THR THR A . n A 1 18 PRO 18 17 17 PRO PRO A . n A 1 19 TRP 19 18 18 TRP TRP A . n A 1 20 MSE 20 19 19 MSE MSE A . n A 1 21 PRO 21 20 20 PRO PRO A . n A 1 22 PHE 22 21 21 PHE PHE A . n A 1 23 ALA 23 22 22 ALA ALA A . n A 1 24 PRO 24 23 23 PRO PRO A . n A 1 25 TYR 25 24 24 TYR TYR A . n A 1 26 SER 26 25 25 SER SER A . n A 1 27 ASN 27 26 26 ASN ASN A . n A 1 28 ASP 28 27 27 ASP ASP A . n A 1 29 VAL 29 28 28 VAL VAL A . n A 1 30 MSE 30 29 29 MSE MSE A . n A 1 31 VAL 31 30 30 VAL VAL A . n A 1 32 LYS 32 31 31 LYS LYS A . n A 1 33 TYR 33 32 32 TYR TYR A . n A 1 34 PHE 34 33 33 PHE PHE A . n A 1 35 LYS 35 34 34 LYS LYS A . n A 1 36 ILE 36 35 35 ILE ILE A . n A 1 37 ASP 37 36 36 ASP ASP A . n A 1 38 PRO 38 37 37 PRO PRO A . n A 1 39 VAL 39 38 38 VAL VAL A . n A 1 40 ARG 40 39 39 ARG ARG A . n A 1 41 GLY 41 40 40 GLY GLY A . n A 1 42 GLU 42 41 41 GLU GLU A . n A 1 43 THR 43 42 42 THR THR A . n A 1 44 ILE 44 43 43 ILE ILE A . n A 1 45 THR 45 44 44 THR THR A . n A 1 46 LEU 46 45 45 LEU LEU A . n A 1 47 LEU 47 46 46 LEU LEU A . n A 1 48 LYS 48 47 47 LYS LYS A . n A 1 49 ALA 49 48 48 ALA ALA A . n A 1 50 PRO 50 49 49 PRO PRO A . n A 1 51 ALA 51 50 50 ALA ALA A . n A 1 52 GLY 52 51 51 GLY GLY A . n A 1 53 MSE 53 52 52 MSE MSE A . n A 1 54 GLU 54 53 53 GLU GLU A . n A 1 55 MSE 55 54 54 MSE MSE A . n A 1 56 PRO 56 55 55 PRO PRO A . n A 1 57 ARG 57 56 56 ARG ARG A . n A 1 58 HIS 58 57 57 HIS HIS A . n A 1 59 HIS 59 58 58 HIS HIS A . n A 1 60 HIS 60 59 59 HIS HIS A . n A 1 61 THR 61 60 60 THR THR A . n A 1 62 GLY 62 61 61 GLY GLY A . n A 1 63 THR 63 62 62 THR THR A . n A 1 64 VAL 64 63 63 VAL VAL A . n A 1 65 ILE 65 64 64 ILE ILE A . n A 1 66 VAL 66 65 65 VAL VAL A . n A 1 67 TYR 67 66 66 TYR TYR A . n A 1 68 THR 68 67 67 THR THR A . n A 1 69 VAL 69 68 68 VAL VAL A . n A 1 70 GLN 70 69 69 GLN GLN A . n A 1 71 GLY 71 70 70 GLY GLY A . n A 1 72 SER 72 71 71 SER SER A . n A 1 73 TRP 73 72 72 TRP TRP A . n A 1 74 ARG 74 73 73 ARG ARG A . n A 1 75 TYR 75 74 74 TYR TYR A . n A 1 76 LYS 76 75 75 LYS LYS A . n A 1 77 GLU 77 76 76 GLU GLU A . n A 1 78 HIS 78 77 77 HIS HIS A . n A 1 79 ASP 79 78 78 ASP ASP A . n A 1 80 TRP 80 79 79 TRP TRP A . n A 1 81 VAL 81 80 80 VAL VAL A . n A 1 82 ALA 82 81 81 ALA ALA A . n A 1 83 HIS 83 82 82 HIS HIS A . n A 1 84 ALA 84 83 83 ALA ALA A . n A 1 85 GLY 85 84 84 GLY GLY A . n A 1 86 SER 86 85 85 SER SER A . n A 1 87 VAL 87 86 86 VAL VAL A . n A 1 88 VAL 88 87 87 VAL VAL A . n A 1 89 TYR 89 88 88 TYR TYR A . n A 1 90 GLU 90 89 89 GLU GLU A . n A 1 91 THR 91 90 90 THR THR A . n A 1 92 ALA 92 91 91 ALA ALA A . n A 1 93 SER 93 92 92 SER SER A . n A 1 94 THR 94 93 93 THR THR A . n A 1 95 ARG 95 94 94 ARG ARG A . n A 1 96 HIS 96 95 95 HIS HIS A . n A 1 97 THR 97 96 96 THR THR A . n A 1 98 PRO 98 97 97 PRO PRO A . n A 1 99 GLN 99 98 98 GLN GLN A . n A 1 100 SER 100 99 99 SER SER A . n A 1 101 ALA 101 100 100 ALA ALA A . n A 1 102 TYR 102 101 101 TYR TYR A . n A 1 103 ALA 103 102 102 ALA ALA A . n A 1 104 GLU 104 103 103 GLU GLU A . n A 1 105 GLY 105 104 104 GLY GLY A . n A 1 106 PRO 106 105 105 PRO PRO A . n A 1 107 ASP 107 106 106 ASP ASP A . n A 1 108 ILE 108 107 107 ILE ILE A . n A 1 109 ILE 109 108 108 ILE ILE A . n A 1 110 THR 110 109 109 THR THR A . n A 1 111 PHE 111 110 110 PHE PHE A . n A 1 112 ASN 112 111 111 ASN ASN A . n A 1 113 ILE 113 112 112 ILE ILE A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 ALA 115 114 114 ALA ALA A . n A 1 116 GLY 116 115 115 GLY GLY A . n A 1 117 GLU 117 116 116 GLU GLU A . n A 1 118 LEU 118 117 117 LEU LEU A . n A 1 119 LEU 119 118 118 LEU LEU A . n A 1 120 TYR 120 119 119 TYR TYR A . n A 1 121 LEU 121 120 120 LEU LEU A . n A 1 122 ASP 122 121 121 ASP ASP A . n A 1 123 ASP 123 122 122 ASP ASP A . n A 1 124 LYS 124 123 123 LYS LYS A . n A 1 125 ASP 125 124 124 ASP ASP A . n A 1 126 ASN 126 125 125 ASN ASN A . n A 1 127 ILE 127 126 126 ILE ILE A . n A 1 128 ILE 128 127 127 ILE ILE A . n A 1 129 ALA 129 128 128 ALA ALA A . n A 1 130 VAL 130 129 129 VAL VAL A . n A 1 131 GLU 131 130 130 GLU GLU A . n A 1 132 ASN 132 131 131 ASN ASN A . n A 1 133 TRP 133 132 132 TRP TRP A . n A 1 134 LYS 134 133 133 LYS LYS A . n A 1 135 THR 135 134 134 THR THR A . n A 1 136 SER 136 135 135 SER SER A . n A 1 137 MSE 137 136 136 MSE MSE A . n A 1 138 ASP 138 137 137 ASP ASP A . n A 1 139 ARG 139 138 138 ARG ARG A . n A 1 140 TYR 140 139 139 TYR TYR A . n A 1 141 LEU 141 140 140 LEU LEU A . n A 1 142 ASN 142 141 141 ASN ASN A . n A 1 143 TYR 143 142 142 TYR TYR A . n A 1 144 CYS 144 143 143 CYS CYS A . n A 1 145 LYS 145 144 144 LYS LYS A . n A 1 146 ALA 146 145 145 ALA ALA A . n A 1 147 HIS 147 146 146 HIS HIS A . n A 1 148 GLY 148 147 147 GLY GLY A . n A 1 149 ILE 149 148 148 ILE ILE A . n A 1 150 ARG 150 149 149 ARG ARG A . n A 1 151 PRO 151 150 150 PRO PRO A . n A 1 152 LYS 152 151 151 LYS LYS A . n A 1 153 ASP 153 152 152 ASP ASP A . n A 1 154 LEU 154 153 153 LEU LEU A . n A 1 155 SER 155 154 154 SER SER A . n A 1 156 THR 156 155 155 THR THR A . n A 1 157 PHE 157 156 156 PHE PHE A . n A 1 158 GLU 158 157 157 GLU GLU A . n A 1 159 GLY 159 158 ? ? ? 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 PEG 1 159 1 PEG PEG A . C 2 PEG 1 160 2 PEG PEG A . D 2 PEG 1 161 3 PEG PEG A . E 2 PEG 1 162 4 PEG PEG A . F 3 HOH 1 163 5 HOH HOH A . F 3 HOH 2 164 6 HOH HOH A . F 3 HOH 3 165 7 HOH HOH A . F 3 HOH 4 166 8 HOH HOH A . F 3 HOH 5 167 9 HOH HOH A . F 3 HOH 6 168 10 HOH HOH A . F 3 HOH 7 169 11 HOH HOH A . F 3 HOH 8 170 12 HOH HOH A . F 3 HOH 9 171 13 HOH HOH A . F 3 HOH 10 172 14 HOH HOH A . F 3 HOH 11 173 15 HOH HOH A . F 3 HOH 12 174 16 HOH HOH A . F 3 HOH 13 175 17 HOH HOH A . F 3 HOH 14 176 18 HOH HOH A . F 3 HOH 15 177 19 HOH HOH A . F 3 HOH 16 178 20 HOH HOH A . F 3 HOH 17 179 21 HOH HOH A . F 3 HOH 18 180 22 HOH HOH A . F 3 HOH 19 181 23 HOH HOH A . F 3 HOH 20 182 24 HOH HOH A . F 3 HOH 21 183 25 HOH HOH A . F 3 HOH 22 184 26 HOH HOH A . F 3 HOH 23 185 27 HOH HOH A . F 3 HOH 24 186 28 HOH HOH A . F 3 HOH 25 187 29 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 20 A MSE 19 ? MET SELENOMETHIONINE 3 A MSE 30 A MSE 29 ? MET SELENOMETHIONINE 4 A MSE 53 A MSE 52 ? MET SELENOMETHIONINE 5 A MSE 55 A MSE 54 ? MET SELENOMETHIONINE 6 A MSE 137 A MSE 136 ? 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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _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)' 16580 ? 1 MORE -42 ? 1 'SSA (A^2)' 23020 ? # 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' 2_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 91.1570000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 5_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 91.1570000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 48.7530000000 4 'crystal symmetry operation' 6_556 x,-y,-z+1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 48.7530000000 # _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 PEG _pdbx_struct_special_symmetry.auth_seq_id 162 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id PEG _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 2008-09-09 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-11 4 'Structure model' 1 3 2019-07-24 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' 'Data collection' 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' 9 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' reflns_shell 2 3 'Structure model' software 3 4 'Structure model' pdbx_struct_special_symmetry 4 4 'Structure model' software 5 4 'Structure model' struct_conn 6 5 'Structure model' database_2 7 5 'Structure model' struct_ref_seq_dif 8 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' '_reflns_shell.percent_possible_all' 2 3 'Structure model' '_software.classification' 3 3 'Structure model' '_software.name' 4 4 'Structure model' '_software.classification' 5 4 'Structure model' '_software.contact_author' 6 4 'Structure model' '_software.contact_author_email' 7 4 'Structure model' '_software.language' 8 4 'Structure model' '_software.location' 9 4 'Structure model' '_software.name' 10 4 'Structure model' '_software.type' 11 4 'Structure model' '_software.version' 12 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 13 5 'Structure model' '_database_2.pdbx_DOI' 14 5 'Structure model' '_database_2.pdbx_database_accession' 15 5 'Structure model' '_struct_ref_seq_dif.details' 16 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 17 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 18 5 '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 34.5814 _pdbx_refine_tls.origin_y 13.8228 _pdbx_refine_tls.origin_z 20.9100 _pdbx_refine_tls.T[1][1] -0.0410 _pdbx_refine_tls.T[2][2] 0.0195 _pdbx_refine_tls.T[3][3] 0.1081 _pdbx_refine_tls.T[1][2] 0.1226 _pdbx_refine_tls.T[1][3] 0.1029 _pdbx_refine_tls.T[2][3] -0.0137 _pdbx_refine_tls.L[1][1] 2.4513 _pdbx_refine_tls.L[2][2] 3.3662 _pdbx_refine_tls.L[3][3] 4.1870 _pdbx_refine_tls.L[1][2] -0.0432 _pdbx_refine_tls.L[1][3] 0.1002 _pdbx_refine_tls.L[2][3] 0.3986 _pdbx_refine_tls.S[1][1] 0.4224 _pdbx_refine_tls.S[2][2] -0.3867 _pdbx_refine_tls.S[3][3] -0.0356 _pdbx_refine_tls.S[1][2] 0.2154 _pdbx_refine_tls.S[1][3] 0.3940 _pdbx_refine_tls.S[2][3] 0.4321 _pdbx_refine_tls.S[2][1] -0.2277 _pdbx_refine_tls.S[3][1] -0.2683 _pdbx_refine_tls.S[3][2] -0.4346 _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_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 157 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 2 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 158 _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 5.2.0019 ? 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 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 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 # _pdbx_entry_details.entry_id 3EBR _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_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 LEU 2 ? CG ? A LEU 3 CG 2 1 Y 1 A LEU 2 ? CD1 ? A LEU 3 CD1 3 1 Y 1 A LEU 2 ? CD2 ? A LEU 3 CD2 4 1 Y 1 A SER 5 ? OG ? A SER 6 OG 5 1 Y 1 A LYS 47 ? CE ? A LYS 48 CE 6 1 Y 1 A LYS 47 ? NZ ? A LYS 48 NZ 7 1 Y 1 A GLU 53 ? CG ? A GLU 54 CG 8 1 Y 1 A GLU 53 ? CD ? A GLU 54 CD 9 1 Y 1 A GLU 53 ? OE1 ? A GLU 54 OE1 10 1 Y 1 A GLU 53 ? OE2 ? A GLU 54 OE2 11 1 Y 1 A LYS 75 ? CE ? A LYS 76 CE 12 1 Y 1 A LYS 75 ? NZ ? A LYS 76 NZ 13 1 Y 1 A ASP 78 ? CG ? A ASP 79 CG 14 1 Y 1 A ASP 78 ? OD1 ? A ASP 79 OD1 15 1 Y 1 A ASP 78 ? OD2 ? A ASP 79 OD2 16 1 Y 1 A ASP 121 ? OD1 ? A ASP 122 OD1 17 1 Y 1 A ASP 121 ? OD2 ? A ASP 122 OD2 18 1 Y 1 A LYS 123 ? CG ? A LYS 124 CG 19 1 Y 1 A LYS 123 ? CD ? A LYS 124 CD 20 1 Y 1 A LYS 123 ? CE ? A LYS 124 CE 21 1 Y 1 A LYS 123 ? NZ ? A LYS 124 NZ 22 1 Y 1 A LYS 144 ? CG ? A LYS 145 CG 23 1 Y 1 A LYS 144 ? CD ? A LYS 145 CD 24 1 Y 1 A LYS 144 ? CE ? A LYS 145 CE 25 1 Y 1 A LYS 144 ? NZ ? A LYS 145 NZ 26 1 Y 1 A ARG 149 ? CD ? A ARG 150 CD 27 1 Y 1 A ARG 149 ? NE ? A ARG 150 NE 28 1 Y 1 A ARG 149 ? CZ ? A ARG 150 CZ 29 1 Y 1 A ARG 149 ? NH1 ? A ARG 150 NH1 30 1 Y 1 A ARG 149 ? NH2 ? A ARG 150 NH2 31 1 Y 1 A SER 154 ? OG ? A SER 155 OG # 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 GLY 158 ? A GLY 159 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'DI(HYDROXYETHYL)ETHER' PEG 3 water HOH #