data_4R1K # _entry.id 4R1K # _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 4R1K pdb_00004r1k 10.2210/pdb4r1k/pdb RCSB RCSB086783 ? ? WWPDB D_1000086783 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-420689 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4R1K _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-08-06 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _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 a hypothetical protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 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 4R1K _cell.length_a 105.646 _cell.length_b 59.318 _cell.length_c 58.411 _cell.angle_alpha 90.000 _cell.angle_beta 101.380 _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 4R1K _symmetry.Int_Tables_number 5 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Uncharacterized protein' 16425.408 2 ? ? ? ? 2 water nat water 18.015 4 ? ? ? ? # _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 ;GDEGNIKENAVR(MSE)(MSE)ECIVNKDSEKLFDFYNKD(MSE)KDNYKDSSLDEIRQLFEYIDGAITSYNYEGKGGGQ EAKNDGIICYYSCHPEFDFTTETGQEYTISFSYHYIWNEHPEYEGIN(MSE)IQICKDGNWGEKLIIGRNYYKE ; _entity_poly.pdbx_seq_one_letter_code_can ;GDEGNIKENAVRMMECIVNKDSEKLFDFYNKDMKDNYKDSSLDEIRQLFEYIDGAITSYNYEGKGGGQEAKNDGIICYYS CHPEFDFTTETGQEYTISFSYHYIWNEHPEYEGINMIQICKDGNWGEKLIIGRNYYKE ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier JCSG-420689 # 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 ASP n 1 3 GLU n 1 4 GLY n 1 5 ASN n 1 6 ILE n 1 7 LYS n 1 8 GLU n 1 9 ASN n 1 10 ALA n 1 11 VAL n 1 12 ARG n 1 13 MSE n 1 14 MSE n 1 15 GLU n 1 16 CYS n 1 17 ILE n 1 18 VAL n 1 19 ASN n 1 20 LYS n 1 21 ASP n 1 22 SER n 1 23 GLU n 1 24 LYS n 1 25 LEU n 1 26 PHE n 1 27 ASP n 1 28 PHE n 1 29 TYR n 1 30 ASN n 1 31 LYS n 1 32 ASP n 1 33 MSE n 1 34 LYS n 1 35 ASP n 1 36 ASN n 1 37 TYR n 1 38 LYS n 1 39 ASP n 1 40 SER n 1 41 SER n 1 42 LEU n 1 43 ASP n 1 44 GLU n 1 45 ILE n 1 46 ARG n 1 47 GLN n 1 48 LEU n 1 49 PHE n 1 50 GLU n 1 51 TYR n 1 52 ILE n 1 53 ASP n 1 54 GLY n 1 55 ALA n 1 56 ILE n 1 57 THR n 1 58 SER n 1 59 TYR n 1 60 ASN n 1 61 TYR n 1 62 GLU n 1 63 GLY n 1 64 LYS n 1 65 GLY n 1 66 GLY n 1 67 GLY n 1 68 GLN n 1 69 GLU n 1 70 ALA n 1 71 LYS n 1 72 ASN n 1 73 ASP n 1 74 GLY n 1 75 ILE n 1 76 ILE n 1 77 CYS n 1 78 TYR n 1 79 TYR n 1 80 SER n 1 81 CYS n 1 82 HIS n 1 83 PRO n 1 84 GLU n 1 85 PHE n 1 86 ASP n 1 87 PHE n 1 88 THR n 1 89 THR n 1 90 GLU n 1 91 THR n 1 92 GLY n 1 93 GLN n 1 94 GLU n 1 95 TYR n 1 96 THR n 1 97 ILE n 1 98 SER n 1 99 PHE n 1 100 SER n 1 101 TYR n 1 102 HIS n 1 103 TYR n 1 104 ILE n 1 105 TRP n 1 106 ASN n 1 107 GLU n 1 108 HIS n 1 109 PRO n 1 110 GLU n 1 111 TYR n 1 112 GLU n 1 113 GLY n 1 114 ILE n 1 115 ASN n 1 116 MSE n 1 117 ILE n 1 118 GLN n 1 119 ILE n 1 120 CYS n 1 121 LYS n 1 122 ASP n 1 123 GLY n 1 124 ASN n 1 125 TRP n 1 126 GLY n 1 127 GLU n 1 128 LYS n 1 129 LEU n 1 130 ILE n 1 131 ILE n 1 132 GLY n 1 133 ARG n 1 134 ASN n 1 135 TYR n 1 136 TYR n 1 137 LYS n 1 138 GLU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene EUBSIR_01394 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'DSM 15702' _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 'Eubacterium siraeum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 428128 _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 PB1 _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 B0MNI9_9FIRM _struct_ref.pdbx_db_accession B0MNI9 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DEGNIKENAVRMMECIVNKDSEKLFDFYNKDMKDNYKDSSLDEIRQLFEYIDGAITSYNYEGKGGGQEAKNDGIICYYSC HPEFDFTTETGQEYTISFSYHYIWNEHPEYEGINMIQICKDGNWGEKLIIGRNYYKE ; _struct_ref.pdbx_align_begin 30 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4R1K A 2 ? 138 ? B0MNI9 30 ? 166 ? 30 166 2 1 4R1K B 2 ? 138 ? B0MNI9 30 ? 166 ? 30 166 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4R1K GLY A 1 ? UNP B0MNI9 ? ? 'expression tag' 0 1 2 4R1K GLY B 1 ? UNP B0MNI9 ? ? 'expression tag' 0 2 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4R1K # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.73 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 54.96 _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 277 _exptl_crystal_grow.pdbx_details ;0.2M magnesium acetate, 30.0% 2-methyl-2,4-pentanediol, 0.1M sodium cacodylate pH 6.5, 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 PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.details 'Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_detector.pdbx_collection_date 2014-05-21 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'single crystal Si(111) bent' _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 0.97939 1.0 2 0.91837 1.0 3 0.97882 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 0.97939,0.91837,0.97882 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4R1K _reflns.d_resolution_high 2.56 _reflns.d_resolution_low 42.844 _reflns.number_obs 11309 _reflns.pdbx_Rmerge_I_obs 0.102 _reflns.pdbx_netI_over_sigmaI 10.160 _reflns.percent_possible_obs 97.500 _reflns.B_iso_Wilson_estimate 53.294 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _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 2.560 2.650 4245 ? 1109 0.652 2.1 ? ? ? ? ? 97.500 1 1 2.650 2.760 4217 ? 1153 0.544 2.5 ? ? ? ? ? 97.800 2 1 2.760 2.880 3713 ? 1047 0.352 3.6 ? ? ? ? ? 95.700 3 1 2.880 3.030 4488 ? 1128 0.240 5.4 ? ? ? ? ? 99.000 4 1 3.030 3.220 4513 ? 1142 0.158 7.6 ? ? ? ? ? 99.300 5 1 3.220 3.470 4444 ? 1142 0.115 10.2 ? ? ? ? ? 98.300 6 1 3.470 3.820 4263 ? 1145 0.090 12.6 ? ? ? ? ? 98.700 7 1 3.820 4.370 3857 ? 1087 0.060 16.8 ? ? ? ? ? 94.400 8 1 4.370 5.480 4446 ? 1143 0.053 19.8 ? ? ? ? ? 98.600 9 1 5.480 ? 4287 ? 1172 0.051 20.4 ? ? ? ? ? 96.100 10 1 # _refine.entry_id 4R1K _refine.ls_d_res_high 2.5600 _refine.ls_d_res_low 42.844 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.7700 _refine.ls_number_reflns_obs 10762 _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. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2551 _refine.ls_R_factor_R_work 0.2528 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2989 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.8000 _refine.ls_number_reflns_R_free 543 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 48.3173 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.6400 _refine.aniso_B[2][2] -5.5500 _refine.aniso_B[3][3] 2.7000 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 4.9500 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9010 _refine.correlation_coeff_Fo_to_Fc_free 0.8720 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.7350 _refine.pdbx_overall_ESU_R_Free 0.3570 _refine.overall_SU_ML 0.2880 _refine.overall_SU_B 29.4880 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _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 96.340 _refine.B_iso_min 30.470 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.750 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _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 2232 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 4 _refine_hist.number_atoms_total 2236 _refine_hist.d_res_high 2.5600 _refine_hist.d_res_low 42.844 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 2285 0.011 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 1990 0.004 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 3074 1.483 1.942 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 4610 1.084 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 269 6.658 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 135 40.455 25.630 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 373 15.548 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 6 28.965 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 295 0.080 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 2665 0.006 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 557 0.004 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 1082 1.664 2.553 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 1081 1.656 2.550 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 1349 2.654 4.773 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.5600 _refine_ls_shell.d_res_low 2.6260 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 98.6800 _refine_ls_shell.number_reflns_R_work 793 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3580 _refine_ls_shell.R_factor_R_free 0.3310 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 820 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.title 'Crystal structure of a NTF2-like protein (EUBSIR_01394) from Eubacterium siraeum DSM 15702 at 2.56 A resolution' _struct.entry_id 4R1K _struct.pdbx_model_type_details ? _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.text ;NTF2-like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION ; _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.entry_id 4R1K # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 4 ? LYS A 20 ? GLY A 32 LYS A 48 1 ? 17 HELX_P HELX_P2 2 ASP A 21 ? ASP A 27 ? ASP A 49 ASP A 55 1 ? 7 HELX_P HELX_P3 3 ASN A 30 ? TYR A 37 ? ASN A 58 TYR A 65 1 ? 8 HELX_P HELX_P4 4 TYR A 37 ? TYR A 51 ? TYR A 65 TYR A 79 1 ? 15 HELX_P HELX_P5 5 HIS A 108 ? GLU A 112 ? HIS A 136 GLU A 140 5 ? 5 HELX_P HELX_P6 6 ASP B 2 ? LYS B 20 ? ASP B 30 LYS B 48 1 ? 19 HELX_P HELX_P7 7 ASP B 21 ? ASP B 27 ? ASP B 49 ASP B 55 1 ? 7 HELX_P HELX_P8 8 ASN B 30 ? TYR B 37 ? ASN B 58 TYR B 65 1 ? 8 HELX_P HELX_P9 9 TYR B 37 ? TYR B 51 ? TYR B 65 TYR B 79 1 ? 15 HELX_P HELX_P10 10 HIS B 108 ? GLU B 112 ? HIS B 136 GLU B 140 5 ? 5 # _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 ARG 12 C ? ? ? 1_555 A MSE 13 N ? ? A ARG 40 A MSE 41 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale2 covale both ? A MSE 13 C ? ? ? 1_555 A MSE 14 N ? ? A MSE 41 A MSE 42 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale3 covale both ? A MSE 14 C ? ? ? 1_555 A GLU 15 N ? ? A MSE 42 A GLU 43 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? A ASP 32 C ? ? ? 1_555 A MSE 33 N ? ? A ASP 60 A MSE 61 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale5 covale both ? A MSE 33 C ? ? ? 1_555 A LYS 34 N ? ? A MSE 61 A LYS 62 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale6 covale both ? A ASN 115 C ? ? ? 1_555 A MSE 116 N ? ? A ASN 143 A MSE 144 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale7 covale both ? A MSE 116 C ? ? ? 1_555 A ILE 117 N ? ? A MSE 144 A ILE 145 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale8 covale both ? B ARG 12 C ? ? ? 1_555 B MSE 13 N ? ? B ARG 40 B MSE 41 1_555 ? ? ? ? ? ? ? 1.349 ? ? covale9 covale both ? B MSE 13 C ? ? ? 1_555 B MSE 14 N ? ? B MSE 41 B MSE 42 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale10 covale both ? B MSE 14 C ? ? ? 1_555 B GLU 15 N ? ? B MSE 42 B GLU 43 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale11 covale both ? B ASP 32 C ? ? ? 1_555 B MSE 33 N ? ? B ASP 60 B MSE 61 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale12 covale both ? B MSE 33 C ? ? ? 1_555 B LYS 34 N ? ? B MSE 61 B LYS 62 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale13 covale both ? B ASN 115 C ? ? ? 1_555 B MSE 116 N ? ? B ASN 143 B MSE 144 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale14 covale both ? B MSE 116 C ? ? ? 1_555 B ILE 117 N ? ? B MSE 144 B ILE 145 1_555 ? ? ? ? ? ? ? 1.343 ? ? # _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 ? 5 ? B ? 5 ? C ? 5 ? D ? 5 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel C 4 5 ? anti-parallel D 1 2 ? anti-parallel D 2 3 ? anti-parallel D 3 4 ? anti-parallel D 4 5 ? 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 ILE A 56 ? TYR A 61 ? ILE A 84 TYR A 89 A 2 GLU A 84 ? THR A 89 ? GLU A 112 THR A 117 A 3 GLU A 94 ? TRP A 105 ? GLU A 122 TRP A 133 A 4 ILE A 75 ? CYS A 81 ? ILE A 103 CYS A 109 A 5 GLU A 69 ? ASN A 72 ? GLU A 97 ASN A 100 B 1 ILE A 56 ? TYR A 61 ? ILE A 84 TYR A 89 B 2 GLU A 84 ? THR A 89 ? GLU A 112 THR A 117 B 3 GLU A 94 ? TRP A 105 ? GLU A 122 TRP A 133 B 4 GLY A 113 ? LYS A 121 ? GLY A 141 LYS A 149 B 5 ASN A 124 ? GLY A 132 ? ASN A 152 GLY A 160 C 1 ILE B 56 ? TYR B 61 ? ILE B 84 TYR B 89 C 2 GLU B 84 ? THR B 89 ? GLU B 112 THR B 117 C 3 GLU B 94 ? TRP B 105 ? GLU B 122 TRP B 133 C 4 ILE B 75 ? CYS B 81 ? ILE B 103 CYS B 109 C 5 GLU B 69 ? ASN B 72 ? GLU B 97 ASN B 100 D 1 ILE B 56 ? TYR B 61 ? ILE B 84 TYR B 89 D 2 GLU B 84 ? THR B 89 ? GLU B 112 THR B 117 D 3 GLU B 94 ? TRP B 105 ? GLU B 122 TRP B 133 D 4 GLY B 113 ? LYS B 121 ? GLY B 141 LYS B 149 D 5 ASN B 124 ? GLY B 132 ? ASN B 152 GLY B 160 # 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 ASN A 60 ? N ASN A 88 O ASP A 86 ? O ASP A 114 A 2 3 N PHE A 87 ? N PHE A 115 O TYR A 95 ? O TYR A 123 A 3 4 O TYR A 101 ? O TYR A 129 N CYS A 81 ? N CYS A 109 A 4 5 O ILE A 75 ? O ILE A 103 N ASN A 72 ? N ASN A 100 B 1 2 N ASN A 60 ? N ASN A 88 O ASP A 86 ? O ASP A 114 B 2 3 N PHE A 87 ? N PHE A 115 O TYR A 95 ? O TYR A 123 B 3 4 N SER A 100 ? N SER A 128 O MSE A 116 ? O MSE A 144 B 4 5 N ILE A 119 ? N ILE A 147 O LEU A 129 ? O LEU A 157 C 1 2 N ASN B 60 ? N ASN B 88 O ASP B 86 ? O ASP B 114 C 2 3 N PHE B 87 ? N PHE B 115 O TYR B 95 ? O TYR B 123 C 3 4 O TYR B 101 ? O TYR B 129 N CYS B 81 ? N CYS B 109 C 4 5 O ILE B 75 ? O ILE B 103 N ASN B 72 ? N ASN B 100 D 1 2 N ASN B 60 ? N ASN B 88 O ASP B 86 ? O ASP B 114 D 2 3 N PHE B 87 ? N PHE B 115 O TYR B 95 ? O TYR B 123 D 3 4 N SER B 100 ? N SER B 128 O MSE B 116 ? O MSE B 144 D 4 5 N ILE B 119 ? N ILE B 147 O LEU B 129 ? O LEU B 157 # _atom_sites.entry_id 4R1K _atom_sites.fract_transf_matrix[1][1] 0.009466 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001905 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.016858 _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] 0.017463 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 0 GLY GLY A . n A 1 2 ASP 2 30 30 ASP ASP A . n A 1 3 GLU 3 31 31 GLU GLU A . n A 1 4 GLY 4 32 32 GLY GLY A . n A 1 5 ASN 5 33 33 ASN ASN A . n A 1 6 ILE 6 34 34 ILE ILE A . n A 1 7 LYS 7 35 35 LYS LYS A . n A 1 8 GLU 8 36 36 GLU GLU A . n A 1 9 ASN 9 37 37 ASN ASN A . n A 1 10 ALA 10 38 38 ALA ALA A . n A 1 11 VAL 11 39 39 VAL VAL A . n A 1 12 ARG 12 40 40 ARG ARG A . n A 1 13 MSE 13 41 41 MSE MSE A . n A 1 14 MSE 14 42 42 MSE MSE A . n A 1 15 GLU 15 43 43 GLU GLU A . n A 1 16 CYS 16 44 44 CYS CYS A . n A 1 17 ILE 17 45 45 ILE ILE A . n A 1 18 VAL 18 46 46 VAL VAL A . n A 1 19 ASN 19 47 47 ASN ASN A . n A 1 20 LYS 20 48 48 LYS LYS A . n A 1 21 ASP 21 49 49 ASP ASP A . n A 1 22 SER 22 50 50 SER SER A . n A 1 23 GLU 23 51 51 GLU GLU A . n A 1 24 LYS 24 52 52 LYS LYS A . n A 1 25 LEU 25 53 53 LEU LEU A . n A 1 26 PHE 26 54 54 PHE PHE A . n A 1 27 ASP 27 55 55 ASP ASP A . n A 1 28 PHE 28 56 56 PHE PHE A . n A 1 29 TYR 29 57 57 TYR TYR A . n A 1 30 ASN 30 58 58 ASN ASN A . n A 1 31 LYS 31 59 59 LYS LYS A . n A 1 32 ASP 32 60 60 ASP ASP A . n A 1 33 MSE 33 61 61 MSE MSE A . n A 1 34 LYS 34 62 62 LYS LYS A . n A 1 35 ASP 35 63 63 ASP ASP A . n A 1 36 ASN 36 64 64 ASN ASN A . n A 1 37 TYR 37 65 65 TYR TYR A . n A 1 38 LYS 38 66 66 LYS LYS A . n A 1 39 ASP 39 67 67 ASP ASP A . n A 1 40 SER 40 68 68 SER SER A . n A 1 41 SER 41 69 69 SER SER A . n A 1 42 LEU 42 70 70 LEU LEU A . n A 1 43 ASP 43 71 71 ASP ASP A . n A 1 44 GLU 44 72 72 GLU GLU A . n A 1 45 ILE 45 73 73 ILE ILE A . n A 1 46 ARG 46 74 74 ARG ARG A . n A 1 47 GLN 47 75 75 GLN GLN A . n A 1 48 LEU 48 76 76 LEU LEU A . n A 1 49 PHE 49 77 77 PHE PHE A . n A 1 50 GLU 50 78 78 GLU GLU A . n A 1 51 TYR 51 79 79 TYR TYR A . n A 1 52 ILE 52 80 80 ILE ILE A . n A 1 53 ASP 53 81 81 ASP ASP A . n A 1 54 GLY 54 82 82 GLY GLY A . n A 1 55 ALA 55 83 83 ALA ALA A . n A 1 56 ILE 56 84 84 ILE ILE A . n A 1 57 THR 57 85 85 THR THR A . n A 1 58 SER 58 86 86 SER SER A . n A 1 59 TYR 59 87 87 TYR TYR A . n A 1 60 ASN 60 88 88 ASN ASN A . n A 1 61 TYR 61 89 89 TYR TYR A . n A 1 62 GLU 62 90 90 GLU GLU A . n A 1 63 GLY 63 91 91 GLY GLY A . n A 1 64 LYS 64 92 92 LYS LYS A . n A 1 65 GLY 65 93 93 GLY GLY A . n A 1 66 GLY 66 94 94 GLY GLY A . n A 1 67 GLY 67 95 95 GLY GLY A . n A 1 68 GLN 68 96 96 GLN GLN A . n A 1 69 GLU 69 97 97 GLU GLU A . n A 1 70 ALA 70 98 98 ALA ALA A . n A 1 71 LYS 71 99 99 LYS LYS A . n A 1 72 ASN 72 100 100 ASN ASN A . n A 1 73 ASP 73 101 101 ASP ASP A . n A 1 74 GLY 74 102 102 GLY GLY A . n A 1 75 ILE 75 103 103 ILE ILE A . n A 1 76 ILE 76 104 104 ILE ILE A . n A 1 77 CYS 77 105 105 CYS CYS A . n A 1 78 TYR 78 106 106 TYR TYR A . n A 1 79 TYR 79 107 107 TYR TYR A . n A 1 80 SER 80 108 108 SER SER A . n A 1 81 CYS 81 109 109 CYS CYS A . n A 1 82 HIS 82 110 110 HIS HIS A . n A 1 83 PRO 83 111 111 PRO PRO A . n A 1 84 GLU 84 112 112 GLU GLU A . n A 1 85 PHE 85 113 113 PHE PHE A . n A 1 86 ASP 86 114 114 ASP ASP A . n A 1 87 PHE 87 115 115 PHE PHE A . n A 1 88 THR 88 116 116 THR THR A . n A 1 89 THR 89 117 117 THR THR A . n A 1 90 GLU 90 118 118 GLU GLU A . n A 1 91 THR 91 119 119 THR THR A . n A 1 92 GLY 92 120 120 GLY GLY A . n A 1 93 GLN 93 121 121 GLN GLN A . n A 1 94 GLU 94 122 122 GLU GLU A . n A 1 95 TYR 95 123 123 TYR TYR A . n A 1 96 THR 96 124 124 THR THR A . n A 1 97 ILE 97 125 125 ILE ILE A . n A 1 98 SER 98 126 126 SER SER A . n A 1 99 PHE 99 127 127 PHE PHE A . n A 1 100 SER 100 128 128 SER SER A . n A 1 101 TYR 101 129 129 TYR TYR A . n A 1 102 HIS 102 130 130 HIS HIS A . n A 1 103 TYR 103 131 131 TYR TYR A . n A 1 104 ILE 104 132 132 ILE ILE A . n A 1 105 TRP 105 133 133 TRP TRP A . n A 1 106 ASN 106 134 134 ASN ASN A . n A 1 107 GLU 107 135 135 GLU GLU A . n A 1 108 HIS 108 136 136 HIS HIS A . n A 1 109 PRO 109 137 137 PRO PRO A . n A 1 110 GLU 110 138 138 GLU GLU A . n A 1 111 TYR 111 139 139 TYR TYR A . n A 1 112 GLU 112 140 140 GLU GLU A . n A 1 113 GLY 113 141 141 GLY GLY A . n A 1 114 ILE 114 142 142 ILE ILE A . n A 1 115 ASN 115 143 143 ASN ASN A . n A 1 116 MSE 116 144 144 MSE MSE A . n A 1 117 ILE 117 145 145 ILE ILE A . n A 1 118 GLN 118 146 146 GLN GLN A . n A 1 119 ILE 119 147 147 ILE ILE A . n A 1 120 CYS 120 148 148 CYS CYS A . n A 1 121 LYS 121 149 149 LYS LYS A . n A 1 122 ASP 122 150 150 ASP ASP A . n A 1 123 GLY 123 151 151 GLY GLY A . n A 1 124 ASN 124 152 152 ASN ASN A . n A 1 125 TRP 125 153 153 TRP TRP A . n A 1 126 GLY 126 154 154 GLY GLY A . n A 1 127 GLU 127 155 155 GLU GLU A . n A 1 128 LYS 128 156 156 LYS LYS A . n A 1 129 LEU 129 157 157 LEU LEU A . n A 1 130 ILE 130 158 158 ILE ILE A . n A 1 131 ILE 131 159 159 ILE ILE A . n A 1 132 GLY 132 160 160 GLY GLY A . n A 1 133 ARG 133 161 161 ARG ARG A . n A 1 134 ASN 134 162 162 ASN ASN A . n A 1 135 TYR 135 163 163 TYR TYR A . n A 1 136 TYR 136 164 ? ? ? A . n A 1 137 LYS 137 165 ? ? ? A . n A 1 138 GLU 138 166 ? ? ? A . n B 1 1 GLY 1 0 0 GLY GLY B . n B 1 2 ASP 2 30 30 ASP ASP B . n B 1 3 GLU 3 31 31 GLU GLU B . n B 1 4 GLY 4 32 32 GLY GLY B . n B 1 5 ASN 5 33 33 ASN ASN B . n B 1 6 ILE 6 34 34 ILE ILE B . n B 1 7 LYS 7 35 35 LYS LYS B . n B 1 8 GLU 8 36 36 GLU GLU B . n B 1 9 ASN 9 37 37 ASN ASN B . n B 1 10 ALA 10 38 38 ALA ALA B . n B 1 11 VAL 11 39 39 VAL VAL B . n B 1 12 ARG 12 40 40 ARG ARG B . n B 1 13 MSE 13 41 41 MSE MSE B . n B 1 14 MSE 14 42 42 MSE MSE B . n B 1 15 GLU 15 43 43 GLU GLU B . n B 1 16 CYS 16 44 44 CYS CYS B . n B 1 17 ILE 17 45 45 ILE ILE B . n B 1 18 VAL 18 46 46 VAL VAL B . n B 1 19 ASN 19 47 47 ASN ASN B . n B 1 20 LYS 20 48 48 LYS LYS B . n B 1 21 ASP 21 49 49 ASP ASP B . n B 1 22 SER 22 50 50 SER SER B . n B 1 23 GLU 23 51 51 GLU GLU B . n B 1 24 LYS 24 52 52 LYS LYS B . n B 1 25 LEU 25 53 53 LEU LEU B . n B 1 26 PHE 26 54 54 PHE PHE B . n B 1 27 ASP 27 55 55 ASP ASP B . n B 1 28 PHE 28 56 56 PHE PHE B . n B 1 29 TYR 29 57 57 TYR TYR B . n B 1 30 ASN 30 58 58 ASN ASN B . n B 1 31 LYS 31 59 59 LYS LYS B . n B 1 32 ASP 32 60 60 ASP ASP B . n B 1 33 MSE 33 61 61 MSE MSE B . n B 1 34 LYS 34 62 62 LYS LYS B . n B 1 35 ASP 35 63 63 ASP ASP B . n B 1 36 ASN 36 64 64 ASN ASN B . n B 1 37 TYR 37 65 65 TYR TYR B . n B 1 38 LYS 38 66 66 LYS LYS B . n B 1 39 ASP 39 67 67 ASP ASP B . n B 1 40 SER 40 68 68 SER SER B . n B 1 41 SER 41 69 69 SER SER B . n B 1 42 LEU 42 70 70 LEU LEU B . n B 1 43 ASP 43 71 71 ASP ASP B . n B 1 44 GLU 44 72 72 GLU GLU B . n B 1 45 ILE 45 73 73 ILE ILE B . n B 1 46 ARG 46 74 74 ARG ARG B . n B 1 47 GLN 47 75 75 GLN GLN B . n B 1 48 LEU 48 76 76 LEU LEU B . n B 1 49 PHE 49 77 77 PHE PHE B . n B 1 50 GLU 50 78 78 GLU GLU B . n B 1 51 TYR 51 79 79 TYR TYR B . n B 1 52 ILE 52 80 80 ILE ILE B . n B 1 53 ASP 53 81 81 ASP ASP B . n B 1 54 GLY 54 82 82 GLY GLY B . n B 1 55 ALA 55 83 83 ALA ALA B . n B 1 56 ILE 56 84 84 ILE ILE B . n B 1 57 THR 57 85 85 THR THR B . n B 1 58 SER 58 86 86 SER SER B . n B 1 59 TYR 59 87 87 TYR TYR B . n B 1 60 ASN 60 88 88 ASN ASN B . n B 1 61 TYR 61 89 89 TYR TYR B . n B 1 62 GLU 62 90 90 GLU GLU B . n B 1 63 GLY 63 91 91 GLY GLY B . n B 1 64 LYS 64 92 92 LYS LYS B . n B 1 65 GLY 65 93 93 GLY GLY B . n B 1 66 GLY 66 94 94 GLY GLY B . n B 1 67 GLY 67 95 95 GLY GLY B . n B 1 68 GLN 68 96 96 GLN GLN B . n B 1 69 GLU 69 97 97 GLU GLU B . n B 1 70 ALA 70 98 98 ALA ALA B . n B 1 71 LYS 71 99 99 LYS LYS B . n B 1 72 ASN 72 100 100 ASN ASN B . n B 1 73 ASP 73 101 101 ASP ASP B . n B 1 74 GLY 74 102 102 GLY GLY B . n B 1 75 ILE 75 103 103 ILE ILE B . n B 1 76 ILE 76 104 104 ILE ILE B . n B 1 77 CYS 77 105 105 CYS CYS B . n B 1 78 TYR 78 106 106 TYR TYR B . n B 1 79 TYR 79 107 107 TYR TYR B . n B 1 80 SER 80 108 108 SER SER B . n B 1 81 CYS 81 109 109 CYS CYS B . n B 1 82 HIS 82 110 110 HIS HIS B . n B 1 83 PRO 83 111 111 PRO PRO B . n B 1 84 GLU 84 112 112 GLU GLU B . n B 1 85 PHE 85 113 113 PHE PHE B . n B 1 86 ASP 86 114 114 ASP ASP B . n B 1 87 PHE 87 115 115 PHE PHE B . n B 1 88 THR 88 116 116 THR THR B . n B 1 89 THR 89 117 117 THR THR B . n B 1 90 GLU 90 118 118 GLU GLU B . n B 1 91 THR 91 119 119 THR THR B . n B 1 92 GLY 92 120 120 GLY GLY B . n B 1 93 GLN 93 121 121 GLN GLN B . n B 1 94 GLU 94 122 122 GLU GLU B . n B 1 95 TYR 95 123 123 TYR TYR B . n B 1 96 THR 96 124 124 THR THR B . n B 1 97 ILE 97 125 125 ILE ILE B . n B 1 98 SER 98 126 126 SER SER B . n B 1 99 PHE 99 127 127 PHE PHE B . n B 1 100 SER 100 128 128 SER SER B . n B 1 101 TYR 101 129 129 TYR TYR B . n B 1 102 HIS 102 130 130 HIS HIS B . n B 1 103 TYR 103 131 131 TYR TYR B . n B 1 104 ILE 104 132 132 ILE ILE B . n B 1 105 TRP 105 133 133 TRP TRP B . n B 1 106 ASN 106 134 134 ASN ASN B . n B 1 107 GLU 107 135 135 GLU GLU B . n B 1 108 HIS 108 136 136 HIS HIS B . n B 1 109 PRO 109 137 137 PRO PRO B . n B 1 110 GLU 110 138 138 GLU GLU B . n B 1 111 TYR 111 139 139 TYR TYR B . n B 1 112 GLU 112 140 140 GLU GLU B . n B 1 113 GLY 113 141 141 GLY GLY B . n B 1 114 ILE 114 142 142 ILE ILE B . n B 1 115 ASN 115 143 143 ASN ASN B . n B 1 116 MSE 116 144 144 MSE MSE B . n B 1 117 ILE 117 145 145 ILE ILE B . n B 1 118 GLN 118 146 146 GLN GLN B . n B 1 119 ILE 119 147 147 ILE ILE B . n B 1 120 CYS 120 148 148 CYS CYS B . n B 1 121 LYS 121 149 149 LYS LYS B . n B 1 122 ASP 122 150 150 ASP ASP B . n B 1 123 GLY 123 151 151 GLY GLY B . n B 1 124 ASN 124 152 152 ASN ASN B . n B 1 125 TRP 125 153 153 TRP TRP B . n B 1 126 GLY 126 154 154 GLY GLY B . n B 1 127 GLU 127 155 155 GLU GLU B . n B 1 128 LYS 128 156 156 LYS LYS B . n B 1 129 LEU 129 157 157 LEU LEU B . n B 1 130 ILE 130 158 158 ILE ILE B . n B 1 131 ILE 131 159 159 ILE ILE B . n B 1 132 GLY 132 160 160 GLY GLY B . n B 1 133 ARG 133 161 161 ARG ARG B . n B 1 134 ASN 134 162 162 ASN ASN B . n B 1 135 TYR 135 163 163 TYR TYR B . n B 1 136 TYR 136 164 164 TYR TYR B . n B 1 137 LYS 137 165 ? ? ? B . n B 1 138 GLU 138 166 ? ? ? B . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 201 200 HOH HOH A . C 2 HOH 2 202 202 HOH HOH A . D 2 HOH 1 201 201 HOH HOH B . D 2 HOH 2 202 203 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 13 A MSE 41 ? MET SELENOMETHIONINE 2 A MSE 14 A MSE 42 ? MET SELENOMETHIONINE 3 A MSE 33 A MSE 61 ? MET SELENOMETHIONINE 4 A MSE 116 A MSE 144 ? MET SELENOMETHIONINE 5 B MSE 13 B MSE 41 ? MET SELENOMETHIONINE 6 B MSE 14 B MSE 42 ? MET SELENOMETHIONINE 7 B MSE 33 B MSE 61 ? MET SELENOMETHIONINE 8 B MSE 116 B MSE 144 ? 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_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 2 1 B,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-10-01 2 'Structure model' 1 1 2014-12-24 3 'Structure model' 1 2 2017-11-22 4 'Structure model' 1 3 2018-01-24 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' 'Structure summary' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Database references' 5 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' citation_author 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn 5 5 'Structure model' struct_ref_seq_dif # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_citation_author.name' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 5 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 13.0220 36.2870 51.1900 0.4134 0.4871 0.1779 -0.0121 -0.1095 -0.0092 2.7026 1.3986 0.9596 0.4183 -0.6859 -0.4718 -0.1395 0.1014 0.0382 0.1557 -0.0083 0.0618 -0.3459 0.1719 -0.0109 'X-RAY DIFFRACTION' 2 ? refined 36.4900 47.4470 36.9940 0.2828 0.5735 0.1392 -0.0233 -0.1076 -0.0261 2.6383 2.3895 2.4496 -0.8736 -0.8392 0.0736 -0.0448 0.0959 -0.0510 0.1844 -0.0302 0.0161 -0.0891 0.0022 -0.0888 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 0 A 163 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 0 B 164 ? . . . . ? # _phasing.method MAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 REFMAC 5.7.0032 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 4R1K _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 30-166 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CG _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 MSE _pdbx_validate_rmsd_angle.auth_seq_id_1 144 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 SE _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 MSE _pdbx_validate_rmsd_angle.auth_seq_id_2 144 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 CE _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 MSE _pdbx_validate_rmsd_angle.auth_seq_id_3 144 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 112.82 _pdbx_validate_rmsd_angle.angle_target_value 98.90 _pdbx_validate_rmsd_angle.angle_deviation 13.92 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.20 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 TRP A 133 ? ? -154.98 86.33 2 1 LYS B 48 ? ? 60.27 60.45 3 1 TRP B 133 ? ? -152.14 87.66 # 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 TYR 164 ? A TYR 136 2 1 Y 1 A LYS 165 ? A LYS 137 3 1 Y 1 A GLU 166 ? A GLU 138 4 1 Y 1 B LYS 165 ? B LYS 137 5 1 Y 1 B GLU 166 ? B GLU 138 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #