data_3CE8 # _entry.id 3CE8 # _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 3CE8 pdb_00003ce8 10.2210/pdb3ce8/pdb RCSB RCSB046668 ? ? WWPDB D_1000046668 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 378293 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3CE8 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-02-28 _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 putative PII-like nitrogen regulatory protein (YP_001048502.1) from Shewanella baltica OS155 at 2.40 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 3CE8 _cell.length_a 71.285 _cell.length_b 71.285 _cell.length_c 71.285 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3CE8 _symmetry.Int_Tables_number 198 _symmetry.space_group_name_H-M 'P 21 3' _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 'Putative PII-like nitrogen regulatory protein' 14031.365 1 ? ? ? ? 2 non-polymer syn 'PHOSPHATE ION' 94.971 2 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 4 water nat water 18.015 9 ? ? ? ? # _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 ;(MSE)GSDKIHHHHHHENLYFQG(MSE)STEQLLVLIAQNDIKDDIVDTLIELEFLSGFSLGNICGFSREHSHFNIKEQV EGYREFCKFEI(MSE)HPAAQQAALLTALALVCKHNPCRYWI(MSE)PIYQNGTLS ; _entity_poly.pdbx_seq_one_letter_code_can ;MGSDKIHHHHHHENLYFQGMSTEQLLVLIAQNDIKDDIVDTLIELEFLSGFSLGNICGFSREHSHFNIKEQVEGYREFCK FEIMHPAAQQAALLTALALVCKHNPCRYWIMPIYQNGTLS ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 378293 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 GLY n 1 3 SER n 1 4 ASP n 1 5 LYS n 1 6 ILE n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 HIS n 1 11 HIS n 1 12 HIS n 1 13 GLU n 1 14 ASN n 1 15 LEU n 1 16 TYR n 1 17 PHE n 1 18 GLN n 1 19 GLY n 1 20 MSE n 1 21 SER n 1 22 THR n 1 23 GLU n 1 24 GLN n 1 25 LEU n 1 26 LEU n 1 27 VAL n 1 28 LEU n 1 29 ILE n 1 30 ALA n 1 31 GLN n 1 32 ASN n 1 33 ASP n 1 34 ILE n 1 35 LYS n 1 36 ASP n 1 37 ASP n 1 38 ILE n 1 39 VAL n 1 40 ASP n 1 41 THR n 1 42 LEU n 1 43 ILE n 1 44 GLU n 1 45 LEU n 1 46 GLU n 1 47 PHE n 1 48 LEU n 1 49 SER n 1 50 GLY n 1 51 PHE n 1 52 SER n 1 53 LEU n 1 54 GLY n 1 55 ASN n 1 56 ILE n 1 57 CYS n 1 58 GLY n 1 59 PHE n 1 60 SER n 1 61 ARG n 1 62 GLU n 1 63 HIS n 1 64 SER n 1 65 HIS n 1 66 PHE n 1 67 ASN n 1 68 ILE n 1 69 LYS n 1 70 GLU n 1 71 GLN n 1 72 VAL n 1 73 GLU n 1 74 GLY n 1 75 TYR n 1 76 ARG n 1 77 GLU n 1 78 PHE n 1 79 CYS n 1 80 LYS n 1 81 PHE n 1 82 GLU n 1 83 ILE n 1 84 MSE n 1 85 HIS n 1 86 PRO n 1 87 ALA n 1 88 ALA n 1 89 GLN n 1 90 GLN n 1 91 ALA n 1 92 ALA n 1 93 LEU n 1 94 LEU n 1 95 THR n 1 96 ALA n 1 97 LEU n 1 98 ALA n 1 99 LEU n 1 100 VAL n 1 101 CYS n 1 102 LYS n 1 103 HIS n 1 104 ASN n 1 105 PRO n 1 106 CYS n 1 107 ARG n 1 108 TYR n 1 109 TRP n 1 110 ILE n 1 111 MSE n 1 112 PRO n 1 113 ILE n 1 114 TYR n 1 115 GLN n 1 116 ASN n 1 117 GLY n 1 118 THR n 1 119 LEU n 1 120 SER 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 Shewanella _entity_src_gen.pdbx_gene_src_gene 'YP_001048502.1, Sbal_0098' _entity_src_gen.gene_src_species 'Shewanella baltica' _entity_src_gen.gene_src_strain OS155 _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 'Shewanella baltica' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 325240 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc BAA-1091 _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 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 A3CYS0_SHEB5 _struct_ref.pdbx_db_accession A3CYS0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSTEQLLVLIAQNDIKDDIVDTLIELEFLSGFSLGNICGFSREHSHFNIKEQVEGYREFCKFEIMHPAAQQAALLTALAL VCKHNPCRYWIMPIYQNGTLS ; _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 3CE8 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 20 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 120 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A3CYS0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 101 _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 101 # 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 3CE8 MSE A 1 ? UNP A3CYS0 ? ? 'expression tag' -18 1 1 3CE8 GLY A 2 ? UNP A3CYS0 ? ? 'expression tag' -17 2 1 3CE8 SER A 3 ? UNP A3CYS0 ? ? 'expression tag' -16 3 1 3CE8 ASP A 4 ? UNP A3CYS0 ? ? 'expression tag' -15 4 1 3CE8 LYS A 5 ? UNP A3CYS0 ? ? 'expression tag' -14 5 1 3CE8 ILE A 6 ? UNP A3CYS0 ? ? 'expression tag' -13 6 1 3CE8 HIS A 7 ? UNP A3CYS0 ? ? 'expression tag' -12 7 1 3CE8 HIS A 8 ? UNP A3CYS0 ? ? 'expression tag' -11 8 1 3CE8 HIS A 9 ? UNP A3CYS0 ? ? 'expression tag' -10 9 1 3CE8 HIS A 10 ? UNP A3CYS0 ? ? 'expression tag' -9 10 1 3CE8 HIS A 11 ? UNP A3CYS0 ? ? 'expression tag' -8 11 1 3CE8 HIS A 12 ? UNP A3CYS0 ? ? 'expression tag' -7 12 1 3CE8 GLU A 13 ? UNP A3CYS0 ? ? 'expression tag' -6 13 1 3CE8 ASN A 14 ? UNP A3CYS0 ? ? 'expression tag' -5 14 1 3CE8 LEU A 15 ? UNP A3CYS0 ? ? 'expression tag' -4 15 1 3CE8 TYR A 16 ? UNP A3CYS0 ? ? 'expression tag' -3 16 1 3CE8 PHE A 17 ? UNP A3CYS0 ? ? 'expression tag' -2 17 1 3CE8 GLN A 18 ? UNP A3CYS0 ? ? 'expression tag' -1 18 1 3CE8 GLY A 19 ? UNP A3CYS0 ? ? 'expression tag' 0 19 # 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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 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 PO4 non-polymer . 'PHOSPHATE ION' ? 'O4 P -3' 94.971 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 3CE8 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 42.83 _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 ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details ;NANODROP, 0.727M Ammonium dihydrogen phosphate, 0.114M Ammonium dihydrogen phosphate, 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 2008-02-03 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent (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 0.97926 1.0 3 0.97879 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, 0.97926, 0.97879' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3CE8 _reflns.d_resolution_high 2.40 _reflns.d_resolution_low 29.099 _reflns.number_obs 4934 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_netI_over_sigmaI 6.300 _reflns.pdbx_Rsym_value 0.065 _reflns.pdbx_redundancy 7.200 _reflns.percent_possible_obs 99.900 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate 68.285 _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 2.40 2.46 ? 2681 ? 0.619 1.2 0.619 ? 7.40 ? 364 100.00 1 1 2.46 2.53 ? 2529 ? 0.493 1.6 0.493 ? 7.50 ? 339 100.00 2 1 2.53 2.60 ? 2533 ? 0.356 2.1 0.356 ? 7.40 ? 342 100.00 3 1 2.60 2.68 ? 2449 ? 0.311 2.4 0.311 ? 7.30 ? 335 100.00 4 1 2.68 2.77 ? 2340 ? 0.252 3.0 0.252 ? 7.40 ? 317 100.00 5 1 2.77 2.87 ? 2302 ? 0.204 3.6 0.204 ? 7.30 ? 314 100.00 6 1 2.87 2.98 ? 2181 ? 0.149 5.0 0.149 ? 7.30 ? 298 100.00 7 1 2.98 3.10 ? 2179 ? 0.111 6.5 0.111 ? 7.40 ? 295 100.00 8 1 3.10 3.24 ? 2008 ? 0.086 7.8 0.086 ? 7.40 ? 273 100.00 9 1 3.24 3.39 ? 1889 ? 0.075 8.7 0.075 ? 7.20 ? 262 100.00 10 1 3.39 3.58 ? 1870 ? 0.073 8.3 0.073 ? 7.20 ? 258 100.00 11 1 3.58 3.79 ? 1792 ? 0.072 8.9 0.072 ? 7.20 ? 248 100.00 12 1 3.79 4.06 ? 1585 ? 0.063 9.2 0.063 ? 7.20 ? 220 100.00 13 1 4.06 4.38 ? 1556 ? 0.050 11.6 0.050 ? 7.10 ? 219 100.00 14 1 4.38 4.80 ? 1413 ? 0.051 10.3 0.051 ? 7.10 ? 200 100.00 15 1 4.80 5.37 ? 1236 ? 0.048 11.9 0.048 ? 7.00 ? 176 100.00 16 1 5.37 6.20 ? 1089 ? 0.052 11.8 0.052 ? 6.80 ? 159 100.00 17 1 6.20 7.59 ? 958 ? 0.054 10.3 0.054 ? 6.70 ? 143 100.00 18 1 7.59 10.73 ? 673 ? 0.049 12.5 0.049 ? 6.10 ? 110 98.90 19 1 10.73 29.099 ? 329 ? 0.048 12.0 0.048 ? 5.30 ? 62 90.50 20 1 # _refine.entry_id 3CE8 _refine.ls_d_res_high 2.400 _refine.ls_d_res_low 29.099 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.820 _refine.ls_number_reflns_obs 4920 _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 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PO4 MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. ; _refine.ls_R_factor_obs 0.198 _refine.ls_R_factor_R_work 0.196 _refine.ls_R_factor_R_free 0.236 _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 230 _refine.B_iso_mean 23.205 _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.947 _refine.pdbx_overall_ESU_R 0.314 _refine.pdbx_overall_ESU_R_Free 0.230 _refine.overall_SU_ML 0.174 _refine.overall_SU_B 16.971 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _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.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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 710 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 9 _refine_hist.number_atoms_total 737 _refine_hist.d_res_high 2.400 _refine_hist.d_res_low 29.099 # 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 743 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 493 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1003 1.765 1.985 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1206 1.582 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 90 3.832 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 33 31.897 24.848 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 128 14.933 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 3 15.180 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 113 0.085 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 802 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 144 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 450 1.235 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 182 0.164 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 724 2.641 4.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 293 4.436 6.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 278 6.496 8.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.400 _refine_ls_shell.d_res_low 2.463 _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 349 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.327 _refine_ls_shell.R_factor_R_free 0.259 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 14 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 363 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3CE8 _struct.title 'Crystal structure of a duf3240 family protein (sbal_0098) from shewanella baltica os155 at 2.40 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Putative pii-like nitrogen regulatory protein, 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 3CE8 # 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 3 ? E N N 3 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details 'AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.' # 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 ILE A 34 ? ILE A 43 ? ILE A 15 ILE A 24 1 ? 10 HELX_P HELX_P2 2 GLN A 89 ? CYS A 101 ? GLN A 70 CYS A 82 1 ? 13 # _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 20 C ? ? ? 1_555 A SER 21 N ? ? A MSE 1 A SER 2 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale2 covale both ? A ILE 83 C ? ? ? 1_555 A MSE 84 N ? ? A ILE 64 A MSE 65 1_555 ? ? ? ? ? ? ? 1.312 ? ? covale3 covale both ? A MSE 84 C ? ? ? 1_555 A HIS 85 N ? ? A MSE 65 A HIS 66 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale4 covale both ? A ILE 110 C ? ? ? 1_555 A MSE 111 N ? ? A ILE 91 A MSE 92 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale5 covale both ? A MSE 111 C ? ? ? 1_555 A PRO 112 N ? ? A MSE 92 A PRO 93 1_555 ? ? ? ? ? ? ? 1.319 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 SER A 52 ? SER A 60 ? SER A 33 SER A 41 A 2 GLY A 74 ? PRO A 86 ? GLY A 55 PRO A 67 A 3 GLU A 23 ? GLN A 31 ? GLU A 4 GLN A 12 A 4 ARG A 107 ? PRO A 112 ? ARG A 88 PRO A 93 # 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 GLY A 54 ? N GLY A 35 O LYS A 80 ? O LYS A 61 A 2 3 O CYS A 79 ? O CYS A 60 N ALA A 30 ? N ALA A 11 A 3 4 N VAL A 27 ? N VAL A 8 O TRP A 109 ? O TRP A 90 # 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 PO4 102 ? 2 'BINDING SITE FOR RESIDUE PO4 A 102' AC2 Software A PO4 103 ? 3 'BINDING SITE FOR RESIDUE PO4 A 103' AC3 Software A EDO 104 ? 7 'BINDING SITE FOR RESIDUE EDO A 104' AC4 Software A EDO 105 ? 5 'BINDING SITE FOR RESIDUE EDO A 105' # 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 2 LYS A 80 ? LYS A 61 . ? 12_565 ? 2 AC1 2 GLU A 82 ? GLU A 63 . ? 6_456 ? 3 AC2 3 ILE A 56 ? ILE A 37 . ? 12_565 ? 4 AC2 3 LYS A 80 ? LYS A 61 . ? 1_555 ? 5 AC2 3 HOH F . ? HOH A 107 . ? 12_565 ? 6 AC3 7 THR A 41 ? THR A 22 . ? 1_555 ? 7 AC3 7 GLU A 44 ? GLU A 25 . ? 1_555 ? 8 AC3 7 LEU A 45 ? LEU A 26 . ? 1_555 ? 9 AC3 7 ALA A 87 ? ALA A 68 . ? 8_645 ? 10 AC3 7 ALA A 88 ? ALA A 69 . ? 8_645 ? 11 AC3 7 GLN A 90 ? GLN A 71 . ? 8_645 ? 12 AC3 7 ALA A 91 ? ALA A 72 . ? 8_645 ? 13 AC4 5 GLY A 50 ? GLY A 31 . ? 1_555 ? 14 AC4 5 PHE A 51 ? PHE A 32 . ? 1_555 ? 15 AC4 5 SER A 52 ? SER A 33 . ? 1_555 ? 16 AC4 5 GLU A 82 ? GLU A 63 . ? 1_555 ? 17 AC4 5 TRP A 109 ? TRP A 90 . ? 6_456 ? # _atom_sites.entry_id 3CE8 _atom_sites.fract_transf_matrix[1][1] 0.014028 _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] 0.014028 _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] 0.014028 _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 P 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 MSE 1 -18 ? ? ? A . n A 1 2 GLY 2 -17 ? ? ? A . n A 1 3 SER 3 -16 ? ? ? A . n A 1 4 ASP 4 -15 ? ? ? A . n A 1 5 LYS 5 -14 ? ? ? A . n A 1 6 ILE 6 -13 ? ? ? A . n A 1 7 HIS 7 -12 ? ? ? A . n A 1 8 HIS 8 -11 ? ? ? A . n A 1 9 HIS 9 -10 ? ? ? A . n A 1 10 HIS 10 -9 ? ? ? A . n A 1 11 HIS 11 -8 ? ? ? A . n A 1 12 HIS 12 -7 ? ? ? A . n A 1 13 GLU 13 -6 ? ? ? A . n A 1 14 ASN 14 -5 ? ? ? A . n A 1 15 LEU 15 -4 ? ? ? A . n A 1 16 TYR 16 -3 ? ? ? A . n A 1 17 PHE 17 -2 ? ? ? A . n A 1 18 GLN 18 -1 ? ? ? A . n A 1 19 GLY 19 0 ? ? ? A . n A 1 20 MSE 20 1 1 MSE MSE A . n A 1 21 SER 21 2 2 SER SER A . n A 1 22 THR 22 3 3 THR THR A . n A 1 23 GLU 23 4 4 GLU GLU A . n A 1 24 GLN 24 5 5 GLN GLN A . n A 1 25 LEU 25 6 6 LEU LEU A . n A 1 26 LEU 26 7 7 LEU LEU A . n A 1 27 VAL 27 8 8 VAL VAL A . n A 1 28 LEU 28 9 9 LEU LEU A . n A 1 29 ILE 29 10 10 ILE ILE A . n A 1 30 ALA 30 11 11 ALA ALA A . n A 1 31 GLN 31 12 12 GLN GLN A . n A 1 32 ASN 32 13 13 ASN ASN A . n A 1 33 ASP 33 14 14 ASP ASP A . n A 1 34 ILE 34 15 15 ILE ILE A . n A 1 35 LYS 35 16 16 LYS LYS A . n A 1 36 ASP 36 17 17 ASP ASP A . n A 1 37 ASP 37 18 18 ASP ASP A . n A 1 38 ILE 38 19 19 ILE ILE A . n A 1 39 VAL 39 20 20 VAL VAL A . n A 1 40 ASP 40 21 21 ASP ASP A . n A 1 41 THR 41 22 22 THR THR A . n A 1 42 LEU 42 23 23 LEU LEU A . n A 1 43 ILE 43 24 24 ILE ILE A . n A 1 44 GLU 44 25 25 GLU GLU A . n A 1 45 LEU 45 26 26 LEU LEU A . n A 1 46 GLU 46 27 27 GLU GLU A . n A 1 47 PHE 47 28 28 PHE PHE A . n A 1 48 LEU 48 29 29 LEU LEU A . n A 1 49 SER 49 30 30 SER SER A . n A 1 50 GLY 50 31 31 GLY GLY A . n A 1 51 PHE 51 32 32 PHE PHE A . n A 1 52 SER 52 33 33 SER SER A . n A 1 53 LEU 53 34 34 LEU LEU A . n A 1 54 GLY 54 35 35 GLY GLY A . n A 1 55 ASN 55 36 36 ASN ASN A . n A 1 56 ILE 56 37 37 ILE ILE A . n A 1 57 CYS 57 38 38 CYS CYS A . n A 1 58 GLY 58 39 39 GLY GLY A . n A 1 59 PHE 59 40 40 PHE PHE A . n A 1 60 SER 60 41 41 SER SER A . n A 1 61 ARG 61 42 42 ARG ARG A . n A 1 62 GLU 62 43 ? ? ? A . n A 1 63 HIS 63 44 ? ? ? A . n A 1 64 SER 64 45 ? ? ? A . n A 1 65 HIS 65 46 ? ? ? A . n A 1 66 PHE 66 47 ? ? ? A . n A 1 67 ASN 67 48 ? ? ? A . n A 1 68 ILE 68 49 ? ? ? A . n A 1 69 LYS 69 50 ? ? ? A . n A 1 70 GLU 70 51 ? ? ? A . n A 1 71 GLN 71 52 ? ? ? A . n A 1 72 VAL 72 53 ? ? ? A . n A 1 73 GLU 73 54 54 GLU GLU A . n A 1 74 GLY 74 55 55 GLY GLY A . n A 1 75 TYR 75 56 56 TYR TYR A . n A 1 76 ARG 76 57 57 ARG ARG A . n A 1 77 GLU 77 58 58 GLU GLU A . n A 1 78 PHE 78 59 59 PHE PHE A . n A 1 79 CYS 79 60 60 CYS CYS A . n A 1 80 LYS 80 61 61 LYS LYS A . n A 1 81 PHE 81 62 62 PHE PHE A . n A 1 82 GLU 82 63 63 GLU GLU A . n A 1 83 ILE 83 64 64 ILE ILE A . n A 1 84 MSE 84 65 65 MSE MSE A . n A 1 85 HIS 85 66 66 HIS HIS A . n A 1 86 PRO 86 67 67 PRO PRO A . n A 1 87 ALA 87 68 68 ALA ALA A . n A 1 88 ALA 88 69 69 ALA ALA A . n A 1 89 GLN 89 70 70 GLN GLN A . n A 1 90 GLN 90 71 71 GLN GLN A . n A 1 91 ALA 91 72 72 ALA ALA A . n A 1 92 ALA 92 73 73 ALA ALA A . n A 1 93 LEU 93 74 74 LEU LEU A . n A 1 94 LEU 94 75 75 LEU LEU A . n A 1 95 THR 95 76 76 THR THR A . n A 1 96 ALA 96 77 77 ALA ALA A . n A 1 97 LEU 97 78 78 LEU LEU A . n A 1 98 ALA 98 79 79 ALA ALA A . n A 1 99 LEU 99 80 80 LEU LEU A . n A 1 100 VAL 100 81 81 VAL VAL A . n A 1 101 CYS 101 82 82 CYS CYS A . n A 1 102 LYS 102 83 83 LYS LYS A . n A 1 103 HIS 103 84 84 HIS HIS A . n A 1 104 ASN 104 85 85 ASN ASN A . n A 1 105 PRO 105 86 86 PRO PRO A . n A 1 106 CYS 106 87 87 CYS CYS A . n A 1 107 ARG 107 88 88 ARG ARG A . n A 1 108 TYR 108 89 89 TYR TYR A . n A 1 109 TRP 109 90 90 TRP TRP A . n A 1 110 ILE 110 91 91 ILE ILE A . n A 1 111 MSE 111 92 92 MSE MSE A . n A 1 112 PRO 112 93 93 PRO PRO A . n A 1 113 ILE 113 94 94 ILE ILE A . n A 1 114 TYR 114 95 95 TYR TYR A . n A 1 115 GLN 115 96 96 GLN GLN A . n A 1 116 ASN 116 97 97 ASN ASN A . n A 1 117 GLY 117 98 98 GLY GLY A . n A 1 118 THR 118 99 99 THR THR A . n A 1 119 LEU 119 100 100 LEU LEU A . n A 1 120 SER 120 101 101 SER SER 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 PO4 1 102 1 PO4 PO4 A . C 2 PO4 1 103 2 PO4 PO4 A . D 3 EDO 1 104 3 EDO EDO A . E 3 EDO 1 105 4 EDO EDO A . F 4 HOH 1 106 5 HOH HOH A . F 4 HOH 2 107 6 HOH HOH A . F 4 HOH 3 108 7 HOH HOH A . F 4 HOH 4 109 8 HOH HOH A . F 4 HOH 5 110 9 HOH HOH A . F 4 HOH 6 111 10 HOH HOH A . F 4 HOH 7 112 11 HOH HOH A . F 4 HOH 8 113 12 HOH HOH A . F 4 HOH 9 114 13 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 20 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 84 A MSE 65 ? MET SELENOMETHIONINE 3 A MSE 111 A MSE 92 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _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)' 6480 ? 1 MORE -31.2 ? 1 'SSA (A^2)' 12250 ? # 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' 6_456 z-1/2,-x+1/2,-y+1 0.0000000000 0.0000000000 1.0000000000 -35.6425000000 -1.0000000000 0.0000000000 0.0000000000 35.6425000000 0.0000000000 -1.0000000000 0.0000000000 71.2850000000 3 'crystal symmetry operation' 12_565 -y+1/2,-z+1,x+1/2 0.0000000000 -1.0000000000 0.0000000000 35.6425000000 0.0000000000 0.0000000000 -1.0000000000 71.2850000000 1.0000000000 0.0000000000 0.0000000000 35.6425000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A PO4 102 ? B PO4 . 2 1 A PO4 102 ? B PO4 . 3 1 A PO4 103 ? C PO4 . # 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 2008-03-11 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 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' 'Source and taxonomy' 3 2 'Structure model' 'Version format compliance' 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' software 2 4 'Structure model' pdbx_struct_special_symmetry 3 4 'Structure model' software 4 4 'Structure model' struct_conn 5 5 'Structure model' database_2 6 5 'Structure model' struct_ref_seq_dif 7 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 22.8210 _pdbx_refine_tls.origin_y 6.6490 _pdbx_refine_tls.origin_z 48.5800 _pdbx_refine_tls.T[1][1] 0.3568 _pdbx_refine_tls.T[2][2] 0.4462 _pdbx_refine_tls.T[3][3] 0.3701 _pdbx_refine_tls.T[1][2] 0.0438 _pdbx_refine_tls.T[1][3] -0.0840 _pdbx_refine_tls.T[2][3] 0.0111 _pdbx_refine_tls.L[1][1] 3.5470 _pdbx_refine_tls.L[2][2] 7.1584 _pdbx_refine_tls.L[3][3] 6.9322 _pdbx_refine_tls.L[1][2] 0.3316 _pdbx_refine_tls.L[1][3] -0.6873 _pdbx_refine_tls.L[2][3] 2.6614 _pdbx_refine_tls.S[1][1] -0.2829 _pdbx_refine_tls.S[2][2] 0.0807 _pdbx_refine_tls.S[3][3] 0.2021 _pdbx_refine_tls.S[1][2] 0.5556 _pdbx_refine_tls.S[1][3] 0.0073 _pdbx_refine_tls.S[2][3] 0.1361 _pdbx_refine_tls.S[2][1] -0.6405 _pdbx_refine_tls.S[3][1] -0.3156 _pdbx_refine_tls.S[3][2] -0.1198 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _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 _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.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 20 A 61 ? A 1 A 42 'X-RAY DIFFRACTION' ? 2 1 A 73 A 120 ? A 54 A 101 'X-RAY DIFFRACTION' ? # _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 5.4.0067 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran_77 ? 5 PDB_EXTRACT 3.000 'July 2, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 MAR345 CCD ? ? ? ? 'data collection' ? ? ? 7 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 8 SHARP . ? ? ? ? phasing ? ? ? 9 SHELXD . ? ? ? ? phasing ? ? ? 10 # _pdbx_entry_details.entry_id 3CE8 _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 CYS _pdbx_validate_rmsd_bond.auth_seq_id_1 38 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 SG _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 CYS _pdbx_validate_rmsd_bond.auth_seq_id_2 38 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.691 _pdbx_validate_rmsd_bond.bond_target_value 1.812 _pdbx_validate_rmsd_bond.bond_deviation -0.121 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.016 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 SER A 41 ? ? 178.27 172.13 2 1 ARG A 57 ? ? 178.81 -176.49 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 83 ? CE ? A LYS 102 CE 2 1 Y 1 A LYS 83 ? NZ ? A LYS 102 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MSE -18 ? A MSE 1 2 1 Y 1 A GLY -17 ? A GLY 2 3 1 Y 1 A SER -16 ? A SER 3 4 1 Y 1 A ASP -15 ? A ASP 4 5 1 Y 1 A LYS -14 ? A LYS 5 6 1 Y 1 A ILE -13 ? A ILE 6 7 1 Y 1 A HIS -12 ? A HIS 7 8 1 Y 1 A HIS -11 ? A HIS 8 9 1 Y 1 A HIS -10 ? A HIS 9 10 1 Y 1 A HIS -9 ? A HIS 10 11 1 Y 1 A HIS -8 ? A HIS 11 12 1 Y 1 A HIS -7 ? A HIS 12 13 1 Y 1 A GLU -6 ? A GLU 13 14 1 Y 1 A ASN -5 ? A ASN 14 15 1 Y 1 A LEU -4 ? A LEU 15 16 1 Y 1 A TYR -3 ? A TYR 16 17 1 Y 1 A PHE -2 ? A PHE 17 18 1 Y 1 A GLN -1 ? A GLN 18 19 1 Y 1 A GLY 0 ? A GLY 19 20 1 Y 1 A GLU 43 ? A GLU 62 21 1 Y 1 A HIS 44 ? A HIS 63 22 1 Y 1 A SER 45 ? A SER 64 23 1 Y 1 A HIS 46 ? A HIS 65 24 1 Y 1 A PHE 47 ? A PHE 66 25 1 Y 1 A ASN 48 ? A ASN 67 26 1 Y 1 A ILE 49 ? A ILE 68 27 1 Y 1 A LYS 50 ? A LYS 69 28 1 Y 1 A GLU 51 ? A GLU 70 29 1 Y 1 A GLN 52 ? A GLN 71 30 1 Y 1 A VAL 53 ? A VAL 72 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PHOSPHATE ION' PO4 3 1,2-ETHANEDIOL EDO 4 water HOH #