data_2RFP # _entry.id 2RFP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2RFP RCSB RCSB044802 WWPDB D_1000044802 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2010-05-26 _pdbx_database_PDB_obs_spr.pdb_id 3MQU _pdbx_database_PDB_obs_spr.replace_pdb_id 2RFP _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 378014 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2RFP _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-10-01 _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_sf OBS _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 ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of Putative NTP Pyrophosphohydrolase (YP_189071.1) from Exiguobacterium sibiricum 255-15 at 1.74 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 # _cell.entry_id 2RFP _cell.length_a 52.126 _cell.length_b 69.077 _cell.length_c 50.197 _cell.angle_alpha 90.000 _cell.angle_beta 111.770 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 2RFP _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 'Putative NTP pyrophosphohydrolase' 19397.064 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 135 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;G(MSE)KQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVK KSLKETYPVTEVERLVGQGDALTDALYFI(MSE)GSFVEAGLEPGPLFEIVQQAN(MSE)AKLGPDGQPIFRESDQKV (MSE)KPDGWLPPEPQLEAEVVRQ(MSE)KEKA ; _entity_poly.pdbx_seq_one_letter_code_can ;GMKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLK ETYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLE AEVVRQMKEKA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 378014 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 MSE n 1 3 LYS n 1 4 GLN n 1 5 PRO n 1 6 ASN n 1 7 TYR n 1 8 TYR n 1 9 GLN n 1 10 ASP n 1 11 VAL n 1 12 LYS n 1 13 GLN n 1 14 PHE n 1 15 HIS n 1 16 GLN n 1 17 THR n 1 18 PHE n 1 19 HIS n 1 20 HIS n 1 21 PRO n 1 22 GLY n 1 23 ALA n 1 24 ASP n 1 25 GLN n 1 26 PRO n 1 27 THR n 1 28 ALA n 1 29 ILE n 1 30 PRO n 1 31 LEU n 1 32 ASP n 1 33 ARG n 1 34 GLY n 1 35 VAL n 1 36 LYS n 1 37 ARG n 1 38 ALA n 1 39 THR n 1 40 TRP n 1 41 THR n 1 42 ALA n 1 43 GLU n 1 44 GLU n 1 45 ALA n 1 46 VAL n 1 47 VAL n 1 48 GLU n 1 49 PHE n 1 50 LEU n 1 51 HIS n 1 52 GLN n 1 53 SER n 1 54 SER n 1 55 GLN n 1 56 ASN n 1 57 GLU n 1 58 THR n 1 59 GLU n 1 60 PHE n 1 61 LEU n 1 62 ALA n 1 63 ALA n 1 64 ILE n 1 65 GLU n 1 66 THR n 1 67 PHE n 1 68 LYS n 1 69 ALA n 1 70 GLY n 1 71 LEU n 1 72 ASP n 1 73 GLN n 1 74 ALA n 1 75 VAL n 1 76 LYS n 1 77 LYS n 1 78 SER n 1 79 LEU n 1 80 LYS n 1 81 GLU n 1 82 THR n 1 83 TYR n 1 84 PRO n 1 85 VAL n 1 86 THR n 1 87 GLU n 1 88 VAL n 1 89 GLU n 1 90 ARG n 1 91 LEU n 1 92 VAL n 1 93 GLY n 1 94 GLN n 1 95 GLY n 1 96 ASP n 1 97 ALA n 1 98 LEU n 1 99 THR n 1 100 ASP n 1 101 ALA n 1 102 LEU n 1 103 TYR n 1 104 PHE n 1 105 ILE n 1 106 MSE n 1 107 GLY n 1 108 SER n 1 109 PHE n 1 110 VAL n 1 111 GLU n 1 112 ALA n 1 113 GLY n 1 114 LEU n 1 115 GLU n 1 116 PRO n 1 117 GLY n 1 118 PRO n 1 119 LEU n 1 120 PHE n 1 121 GLU n 1 122 ILE n 1 123 VAL n 1 124 GLN n 1 125 GLN n 1 126 ALA n 1 127 ASN n 1 128 MSE n 1 129 ALA n 1 130 LYS n 1 131 LEU n 1 132 GLY n 1 133 PRO n 1 134 ASP n 1 135 GLY n 1 136 GLN n 1 137 PRO n 1 138 ILE n 1 139 PHE n 1 140 ARG n 1 141 GLU n 1 142 SER n 1 143 ASP n 1 144 GLN n 1 145 LYS n 1 146 VAL n 1 147 MSE n 1 148 LYS n 1 149 PRO n 1 150 ASP n 1 151 GLY n 1 152 TRP n 1 153 LEU n 1 154 PRO n 1 155 PRO n 1 156 GLU n 1 157 PRO n 1 158 GLN n 1 159 LEU n 1 160 GLU n 1 161 ALA n 1 162 GLU n 1 163 VAL n 1 164 VAL n 1 165 ARG n 1 166 GLN n 1 167 MSE n 1 168 LYS n 1 169 GLU n 1 170 LYS n 1 171 ALA 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 'YP_189071.1, ExigDRAFT_0305' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 255-15 _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 'Exiguobacterium sibiricum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 262543 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain HK100 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name speedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q41AV7_9BACI _struct_ref.pdbx_db_accession Q41AV7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKQPNYYQDVKQFHQTFHHPGADQPTAIPLDRGVKRATWTAEEAVVEFLHQSSQNETEFLAAIETFKAGLDQAVKKSLKE TYPVTEVERLVGQGDALTDALYFIMGSFVEAGLEPGPLFEIVQQANMAKLGPDGQPIFRESDQKVMKPDGWLPPEPQLEA EVVRQMKEKA ; _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 2RFP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 171 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q41AV7 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 170 _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 170 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2RFP _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q41AV7 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'LEADER SEQUENCE' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 2RFP # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.16 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.14 _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 7.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details 'NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.details KOHZU _diffrn_detector.pdbx_collection_date 2007-08-30 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double crystal Si(111)' _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 1.0000 1.0 2 0.9798 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_wavelength_list '1.0000, 0.9798' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ALS # _reflns.entry_id 2RFP _reflns.d_resolution_high 1.74 _reflns.d_resolution_low 27.756 _reflns.number_obs 14000 _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_netI_over_sigmaI 7.900 _reflns.pdbx_Rsym_value 0.060 _reflns.pdbx_redundancy 2.400 _reflns.percent_possible_obs 82.700 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 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_diffrn_id _reflns_shell.pdbx_ordinal 1.74 1.79 ? 271 ? 0.675 1.2 0.675 ? 1.10 ? 255 20.60 ? 1 1.79 1.83 ? 515 ? 0.451 1.6 0.451 ? 1.10 ? 453 38.30 ? 2 1.83 1.89 ? 915 ? 0.328 2.3 0.328 ? 1.30 ? 693 57.80 ? 3 1.89 1.95 ? 1487 ? 0.273 1.4 0.273 ? 1.70 ? 883 77.80 ? 4 1.95 2.01 ? 1948 ? 0.193 3.9 0.193 ? 2.00 ? 973 88.30 ? 5 2.01 2.08 ? 2314 ? 0.172 4.3 0.172 ? 2.30 ? 1018 93.10 ? 6 2.08 2.16 ? 2406 ? 0.141 5.1 0.141 ? 2.50 ? 981 94.50 ? 7 2.16 2.25 ? 2472 ? 0.117 6.1 0.117 ? 2.60 ? 966 97.20 ? 8 2.25 2.35 ? 2449 ? 0.111 4.6 0.111 ? 2.60 ? 937 97.80 ? 9 2.35 2.46 ? 2372 ? 0.085 7.7 0.085 ? 2.60 ? 902 98.40 ? 10 2.46 2.59 ? 2322 ? 0.081 8.0 0.081 ? 2.70 ? 867 98.30 ? 11 2.59 2.75 ? 2227 ? 0.066 9.6 0.066 ? 2.70 ? 814 98.10 ? 12 2.75 2.94 ? 2122 ? 0.058 10.6 0.058 ? 2.80 ? 770 98.40 ? 13 2.94 3.18 ? 1924 ? 0.052 10.8 0.052 ? 2.70 ? 710 98.60 ? 14 3.18 3.48 ? 1810 ? 0.050 11.1 0.050 ? 2.70 ? 663 98.50 ? 15 3.48 3.89 ? 1590 ? 0.053 11.7 0.053 ? 2.60 ? 601 98.40 ? 16 3.89 4.49 ? 1331 ? 0.050 11.6 0.050 ? 2.50 ? 524 97.80 ? 17 4.49 5.50 ? 1199 ? 0.038 15.2 0.038 ? 2.70 ? 441 98.60 ? 18 5.50 7.78 ? 1013 ? 0.037 14.8 0.037 ? 2.90 ? 352 99.10 ? 19 7.78 27.756 ? 548 ? 0.037 13.3 0.037 ? 2.80 ? 197 96.50 ? 20 # _refine.entry_id 2RFP _refine.ls_d_res_high 1.740 _refine.ls_d_res_low 27.756 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 82.410 _refine.ls_number_reflns_obs 14000 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) FROM THE CRYSTALLIZATION BUFFER WAS MODELED INTO THE STRUCTURE. 4. THE NOMINAL RESOLUTION IS 1.90 A WITH 1573 OBSERVED REFLECTIONS BETWEEN 1.90-1.74 (40.4% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. ; _refine.ls_R_factor_obs 0.184 _refine.ls_R_factor_R_work 0.182 _refine.ls_R_factor_R_free 0.232 _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 715 _refine.B_iso_mean 20.312 _refine.aniso_B[1][1] 3.850 _refine.aniso_B[2][2] -1.290 _refine.aniso_B[3][3] -1.640 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 1.240 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.963 _refine.correlation_coeff_Fo_to_Fc_free 0.939 _refine.pdbx_overall_ESU_R 0.155 _refine.pdbx_overall_ESU_R_Free 0.146 _refine.overall_SU_ML 0.102 _refine.overall_SU_B 3.326 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.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.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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _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 1323 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 135 _refine_hist.number_atoms_total 1464 _refine_hist.d_res_high 1.740 _refine_hist.d_res_low 27.756 # 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 1382 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 941 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1878 1.539 1.963 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2308 1.013 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 172 6.748 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 67 36.142 25.373 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 228 13.223 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 6 15.562 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 201 0.094 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1554 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 262 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 301 0.223 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 881 0.195 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 701 0.183 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 644 0.084 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 91 0.166 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 13 0.170 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 68 0.221 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 19 0.235 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 950 2.409 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 339 0.622 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1386 3.145 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 571 5.685 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 492 7.494 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.740 _refine_ls_shell.d_res_low 1.786 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 20.680 _refine_ls_shell.number_reflns_R_work 243 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.333 _refine_ls_shell.R_factor_R_free 0.252 _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 257 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2RFP _struct.title 'Crystal structure of Putative NTP Pyrophosphohydrolase (YP_001813558.1) from Exiguobacterium sibiricum 255-15 at 1.74 A resolution' _struct.pdbx_descriptor 'Putative NTP pyrophosphohydrolase' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Putative NTP Pyrophosphohydrolase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, HYDROLASE ; _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.entry_id 2RFP # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details 'SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A 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 ASN A 6 ? PHE A 18 ? ASN A 5 PHE A 17 1 ? 13 HELX_P HELX_P2 2 PRO A 30 ? VAL A 46 ? PRO A 29 VAL A 45 1 ? 17 HELX_P HELX_P3 3 VAL A 46 ? SER A 53 ? VAL A 45 SER A 52 1 ? 8 HELX_P HELX_P4 4 ASN A 56 ? LYS A 80 ? ASN A 55 LYS A 79 1 ? 25 HELX_P HELX_P5 5 THR A 86 ? GLY A 113 ? THR A 85 GLY A 112 1 ? 28 HELX_P HELX_P6 6 GLU A 115 ? ALA A 129 ? GLU A 114 ALA A 128 1 ? 15 HELX_P HELX_P7 7 PRO A 155 ? ALA A 171 ? PRO A 154 ALA A 170 1 ? 17 # _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 covale1 covale ? ? A ILE 105 C A ? ? 1_555 A MSE 106 N ? ? A ILE 104 A MSE 105 1_555 ? ? ? ? ? ? ? 1.329 ? covale2 covale ? ? A ILE 105 C B ? ? 1_555 A MSE 106 N ? ? A ILE 104 A MSE 105 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale ? ? A MSE 106 C ? ? ? 1_555 A GLY 107 N ? ? A MSE 105 A GLY 106 1_555 ? ? ? ? ? ? ? 1.328 ? covale4 covale ? ? A ASN 127 C ? ? ? 1_555 A MSE 128 N ? ? A ASN 126 A MSE 127 1_555 ? ? ? ? ? ? ? 1.333 ? covale5 covale ? ? A MSE 128 C ? ? ? 1_555 A ALA 129 N ? ? A MSE 127 A ALA 128 1_555 ? ? ? ? ? ? ? 1.329 ? covale6 covale ? ? A VAL 146 C ? ? ? 1_555 A MSE 147 N ? ? A VAL 145 A MSE 146 1_555 ? ? ? ? ? ? ? 1.328 ? covale7 covale ? ? A MSE 147 C ? ? ? 1_555 A LYS 148 N ? ? A MSE 146 A LYS 147 1_555 ? ? ? ? ? ? ? 1.330 ? covale8 covale ? ? A GLN 166 C ? ? ? 1_555 A MSE 167 N ? ? A GLN 165 A MSE 166 1_555 ? ? ? ? ? ? ? 1.326 ? covale9 covale ? ? A MSE 167 C ? ? ? 1_555 A LYS 168 N ? ? A MSE 166 A LYS 167 1_555 ? ? ? ? ? ? ? 1.336 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLU _struct_mon_prot_cis.label_seq_id 141 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLU _struct_mon_prot_cis.auth_seq_id 140 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 SER _struct_mon_prot_cis.pdbx_label_seq_id_2 142 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 SER _struct_mon_prot_cis.pdbx_auth_seq_id_2 141 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 9.78 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 5 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 171' # 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 5 PHE A 14 ? PHE A 13 . ? 1_555 ? 2 AC1 5 HIS A 15 ? HIS A 14 . ? 1_555 ? 3 AC1 5 HIS A 20 ? HIS A 19 . ? 1_555 ? 4 AC1 5 ARG A 37 ? ARG A 36 . ? 1_555 ? 5 AC1 5 GLY A 107 ? GLY A 106 . ? 2_556 ? # _atom_sites.entry_id 2RFP _atom_sites.fract_transf_matrix[1][1] 0.019184 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007662 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014477 _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] 0.021452 _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 SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 ? ? ? A . n A 1 3 LYS 3 2 2 LYS LYS A . n A 1 4 GLN 4 3 3 GLN GLN A . n A 1 5 PRO 5 4 4 PRO PRO A . n A 1 6 ASN 6 5 5 ASN ASN A . n A 1 7 TYR 7 6 6 TYR TYR A . n A 1 8 TYR 8 7 7 TYR TYR A . n A 1 9 GLN 9 8 8 GLN GLN A . n A 1 10 ASP 10 9 9 ASP ASP A . n A 1 11 VAL 11 10 10 VAL VAL A . n A 1 12 LYS 12 11 11 LYS LYS A . n A 1 13 GLN 13 12 12 GLN GLN A . n A 1 14 PHE 14 13 13 PHE PHE A . n A 1 15 HIS 15 14 14 HIS HIS A . n A 1 16 GLN 16 15 15 GLN GLN A . n A 1 17 THR 17 16 16 THR THR A . n A 1 18 PHE 18 17 17 PHE PHE A . n A 1 19 HIS 19 18 18 HIS HIS A . n A 1 20 HIS 20 19 19 HIS HIS A . n A 1 21 PRO 21 20 20 PRO PRO A . n A 1 22 GLY 22 21 21 GLY GLY A . n A 1 23 ALA 23 22 22 ALA ALA A . n A 1 24 ASP 24 23 23 ASP ASP A . n A 1 25 GLN 25 24 24 GLN GLN A . n A 1 26 PRO 26 25 25 PRO PRO A . n A 1 27 THR 27 26 26 THR THR A . n A 1 28 ALA 28 27 27 ALA ALA A . n A 1 29 ILE 29 28 28 ILE ILE A . n A 1 30 PRO 30 29 29 PRO PRO A . n A 1 31 LEU 31 30 30 LEU LEU A . n A 1 32 ASP 32 31 31 ASP ASP A . n A 1 33 ARG 33 32 32 ARG ARG A . n A 1 34 GLY 34 33 33 GLY GLY A . n A 1 35 VAL 35 34 34 VAL VAL A . n A 1 36 LYS 36 35 35 LYS LYS A . n A 1 37 ARG 37 36 36 ARG ARG A . n A 1 38 ALA 38 37 37 ALA ALA A . n A 1 39 THR 39 38 38 THR THR A . n A 1 40 TRP 40 39 39 TRP TRP A . n A 1 41 THR 41 40 40 THR THR A . n A 1 42 ALA 42 41 41 ALA ALA A . n A 1 43 GLU 43 42 42 GLU GLU A . n A 1 44 GLU 44 43 43 GLU GLU A . n A 1 45 ALA 45 44 44 ALA ALA A . n A 1 46 VAL 46 45 45 VAL VAL A . n A 1 47 VAL 47 46 46 VAL VAL A . n A 1 48 GLU 48 47 47 GLU GLU A . n A 1 49 PHE 49 48 48 PHE PHE A . n A 1 50 LEU 50 49 49 LEU LEU A . n A 1 51 HIS 51 50 50 HIS HIS A . n A 1 52 GLN 52 51 51 GLN GLN A . n A 1 53 SER 53 52 52 SER SER A . n A 1 54 SER 54 53 53 SER SER A . n A 1 55 GLN 55 54 54 GLN GLN A . n A 1 56 ASN 56 55 55 ASN ASN A . n A 1 57 GLU 57 56 56 GLU GLU A . n A 1 58 THR 58 57 57 THR THR A . n A 1 59 GLU 59 58 58 GLU GLU A . n A 1 60 PHE 60 59 59 PHE PHE A . n A 1 61 LEU 61 60 60 LEU LEU A . n A 1 62 ALA 62 61 61 ALA ALA A . n A 1 63 ALA 63 62 62 ALA ALA A . n A 1 64 ILE 64 63 63 ILE ILE A . n A 1 65 GLU 65 64 64 GLU GLU A . n A 1 66 THR 66 65 65 THR THR A . n A 1 67 PHE 67 66 66 PHE PHE A . n A 1 68 LYS 68 67 67 LYS LYS A . n A 1 69 ALA 69 68 68 ALA ALA A . n A 1 70 GLY 70 69 69 GLY GLY A . n A 1 71 LEU 71 70 70 LEU LEU A . n A 1 72 ASP 72 71 71 ASP ASP A . n A 1 73 GLN 73 72 72 GLN GLN A . n A 1 74 ALA 74 73 73 ALA ALA A . n A 1 75 VAL 75 74 74 VAL VAL A . n A 1 76 LYS 76 75 75 LYS LYS A . n A 1 77 LYS 77 76 76 LYS LYS A . n A 1 78 SER 78 77 77 SER SER A . n A 1 79 LEU 79 78 78 LEU LEU A . n A 1 80 LYS 80 79 79 LYS LYS A . n A 1 81 GLU 81 80 80 GLU GLU A . n A 1 82 THR 82 81 81 THR THR A . n A 1 83 TYR 83 82 82 TYR TYR A . n A 1 84 PRO 84 83 83 PRO PRO A . n A 1 85 VAL 85 84 84 VAL VAL A . n A 1 86 THR 86 85 85 THR THR A . n A 1 87 GLU 87 86 86 GLU GLU A . n A 1 88 VAL 88 87 87 VAL VAL A . n A 1 89 GLU 89 88 88 GLU GLU A . n A 1 90 ARG 90 89 89 ARG ARG A . n A 1 91 LEU 91 90 90 LEU LEU A . n A 1 92 VAL 92 91 91 VAL VAL A . n A 1 93 GLY 93 92 92 GLY GLY A . n A 1 94 GLN 94 93 93 GLN GLN A . n A 1 95 GLY 95 94 94 GLY GLY A . n A 1 96 ASP 96 95 95 ASP ASP A . n A 1 97 ALA 97 96 96 ALA ALA A . n A 1 98 LEU 98 97 97 LEU LEU A . n A 1 99 THR 99 98 98 THR THR A . n A 1 100 ASP 100 99 99 ASP ASP A . n A 1 101 ALA 101 100 100 ALA ALA A . n A 1 102 LEU 102 101 101 LEU LEU A . n A 1 103 TYR 103 102 102 TYR TYR A . n A 1 104 PHE 104 103 103 PHE PHE A . n A 1 105 ILE 105 104 104 ILE ILE A . n A 1 106 MSE 106 105 105 MSE MSE A . n A 1 107 GLY 107 106 106 GLY GLY A . n A 1 108 SER 108 107 107 SER SER A . n A 1 109 PHE 109 108 108 PHE PHE A . n A 1 110 VAL 110 109 109 VAL VAL A . n A 1 111 GLU 111 110 110 GLU GLU A . n A 1 112 ALA 112 111 111 ALA ALA A . n A 1 113 GLY 113 112 112 GLY GLY A . n A 1 114 LEU 114 113 113 LEU LEU A . n A 1 115 GLU 115 114 114 GLU GLU A . n A 1 116 PRO 116 115 115 PRO PRO A . n A 1 117 GLY 117 116 116 GLY GLY A . n A 1 118 PRO 118 117 117 PRO PRO A . n A 1 119 LEU 119 118 118 LEU LEU A . n A 1 120 PHE 120 119 119 PHE PHE A . n A 1 121 GLU 121 120 120 GLU GLU A . n A 1 122 ILE 122 121 121 ILE ILE A . n A 1 123 VAL 123 122 122 VAL VAL A . n A 1 124 GLN 124 123 123 GLN GLN A . n A 1 125 GLN 125 124 124 GLN GLN A . n A 1 126 ALA 126 125 125 ALA ALA A . n A 1 127 ASN 127 126 126 ASN ASN A . n A 1 128 MSE 128 127 127 MSE MSE A . n A 1 129 ALA 129 128 128 ALA ALA A . n A 1 130 LYS 130 129 129 LYS LYS A . n A 1 131 LEU 131 130 130 LEU LEU A . n A 1 132 GLY 132 131 131 GLY GLY A . n A 1 133 PRO 133 132 132 PRO PRO A . n A 1 134 ASP 134 133 133 ASP ASP A . n A 1 135 GLY 135 134 134 GLY GLY A . n A 1 136 GLN 136 135 135 GLN GLN A . n A 1 137 PRO 137 136 136 PRO PRO A . n A 1 138 ILE 138 137 137 ILE ILE A . n A 1 139 PHE 139 138 138 PHE PHE A . n A 1 140 ARG 140 139 139 ARG ARG A . n A 1 141 GLU 141 140 140 GLU GLU A . n A 1 142 SER 142 141 141 SER SER A . n A 1 143 ASP 143 142 142 ASP ASP A . n A 1 144 GLN 144 143 143 GLN GLN A . n A 1 145 LYS 145 144 144 LYS LYS A . n A 1 146 VAL 146 145 145 VAL VAL A . n A 1 147 MSE 147 146 146 MSE MSE A . n A 1 148 LYS 148 147 147 LYS LYS A . n A 1 149 PRO 149 148 148 PRO PRO A . n A 1 150 ASP 150 149 149 ASP ASP A . n A 1 151 GLY 151 150 150 GLY GLY A . n A 1 152 TRP 152 151 151 TRP TRP A . n A 1 153 LEU 153 152 152 LEU LEU A . n A 1 154 PRO 154 153 153 PRO PRO A . n A 1 155 PRO 155 154 154 PRO PRO A . n A 1 156 GLU 156 155 155 GLU GLU A . n A 1 157 PRO 157 156 156 PRO PRO A . n A 1 158 GLN 158 157 157 GLN GLN A . n A 1 159 LEU 159 158 158 LEU LEU A . n A 1 160 GLU 160 159 159 GLU GLU A . n A 1 161 ALA 161 160 160 ALA ALA A . n A 1 162 GLU 162 161 161 GLU GLU A . n A 1 163 VAL 163 162 162 VAL VAL A . n A 1 164 VAL 164 163 163 VAL VAL A . n A 1 165 ARG 165 164 164 ARG ARG A . n A 1 166 GLN 166 165 165 GLN GLN A . n A 1 167 MSE 167 166 166 MSE MSE A . n A 1 168 LYS 168 167 167 LYS LYS A . n A 1 169 GLU 169 168 168 GLU GLU A . n A 1 170 LYS 170 169 169 LYS LYS A . n A 1 171 ALA 171 170 170 ALA ALA 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 GOL 1 171 1 GOL GOL A . C 3 HOH 1 172 2 HOH HOH A . C 3 HOH 2 173 3 HOH HOH A . C 3 HOH 3 174 4 HOH HOH A . C 3 HOH 4 175 5 HOH HOH A . C 3 HOH 5 176 6 HOH HOH A . C 3 HOH 6 177 7 HOH HOH A . C 3 HOH 7 178 8 HOH HOH A . C 3 HOH 8 179 9 HOH HOH A . C 3 HOH 9 180 10 HOH HOH A . C 3 HOH 10 181 11 HOH HOH A . C 3 HOH 11 182 12 HOH HOH A . C 3 HOH 12 183 13 HOH HOH A . C 3 HOH 13 184 14 HOH HOH A . C 3 HOH 14 185 15 HOH HOH A . C 3 HOH 15 186 16 HOH HOH A . C 3 HOH 16 187 17 HOH HOH A . C 3 HOH 17 188 18 HOH HOH A . C 3 HOH 18 189 19 HOH HOH A . C 3 HOH 19 190 20 HOH HOH A . C 3 HOH 20 191 21 HOH HOH A . C 3 HOH 21 192 22 HOH HOH A . C 3 HOH 22 193 23 HOH HOH A . C 3 HOH 23 194 24 HOH HOH A . C 3 HOH 24 195 25 HOH HOH A . C 3 HOH 25 196 26 HOH HOH A . C 3 HOH 26 197 27 HOH HOH A . C 3 HOH 27 198 28 HOH HOH A . C 3 HOH 28 199 29 HOH HOH A . C 3 HOH 29 200 30 HOH HOH A . C 3 HOH 30 201 31 HOH HOH A . C 3 HOH 31 202 32 HOH HOH A . C 3 HOH 32 203 33 HOH HOH A . C 3 HOH 33 204 34 HOH HOH A . C 3 HOH 34 205 35 HOH HOH A . C 3 HOH 35 206 36 HOH HOH A . C 3 HOH 36 207 37 HOH HOH A . C 3 HOH 37 208 38 HOH HOH A . C 3 HOH 38 209 39 HOH HOH A . C 3 HOH 39 210 40 HOH HOH A . C 3 HOH 40 211 41 HOH HOH A . C 3 HOH 41 212 42 HOH HOH A . C 3 HOH 42 213 43 HOH HOH A . C 3 HOH 43 214 44 HOH HOH A . C 3 HOH 44 215 45 HOH HOH A . C 3 HOH 45 216 46 HOH HOH A . C 3 HOH 46 217 47 HOH HOH A . C 3 HOH 47 218 48 HOH HOH A . C 3 HOH 48 219 49 HOH HOH A . C 3 HOH 49 220 50 HOH HOH A . C 3 HOH 50 221 51 HOH HOH A . C 3 HOH 51 222 52 HOH HOH A . C 3 HOH 52 223 53 HOH HOH A . C 3 HOH 53 224 54 HOH HOH A . C 3 HOH 54 225 55 HOH HOH A . C 3 HOH 55 226 56 HOH HOH A . C 3 HOH 56 227 57 HOH HOH A . C 3 HOH 57 228 58 HOH HOH A . C 3 HOH 58 229 59 HOH HOH A . C 3 HOH 59 230 60 HOH HOH A . C 3 HOH 60 231 61 HOH HOH A . C 3 HOH 61 232 62 HOH HOH A . C 3 HOH 62 233 63 HOH HOH A . C 3 HOH 63 234 64 HOH HOH A . C 3 HOH 64 235 65 HOH HOH A . C 3 HOH 65 236 66 HOH HOH A . C 3 HOH 66 237 67 HOH HOH A . C 3 HOH 67 238 68 HOH HOH A . C 3 HOH 68 239 69 HOH HOH A . C 3 HOH 69 240 70 HOH HOH A . C 3 HOH 70 241 71 HOH HOH A . C 3 HOH 71 242 72 HOH HOH A . C 3 HOH 72 243 73 HOH HOH A . C 3 HOH 73 244 74 HOH HOH A . C 3 HOH 74 245 75 HOH HOH A . C 3 HOH 75 246 76 HOH HOH A . C 3 HOH 76 247 77 HOH HOH A . C 3 HOH 77 248 78 HOH HOH A . C 3 HOH 78 249 79 HOH HOH A . C 3 HOH 79 250 80 HOH HOH A . C 3 HOH 80 251 81 HOH HOH A . C 3 HOH 81 252 82 HOH HOH A . C 3 HOH 82 253 83 HOH HOH A . C 3 HOH 83 254 84 HOH HOH A . C 3 HOH 84 255 85 HOH HOH A . C 3 HOH 85 256 86 HOH HOH A . C 3 HOH 86 257 87 HOH HOH A . C 3 HOH 87 258 88 HOH HOH A . C 3 HOH 88 259 89 HOH HOH A . C 3 HOH 89 260 90 HOH HOH A . C 3 HOH 90 261 91 HOH HOH A . C 3 HOH 91 262 92 HOH HOH A . C 3 HOH 92 263 93 HOH HOH A . C 3 HOH 93 264 94 HOH HOH A . C 3 HOH 94 265 95 HOH HOH A . C 3 HOH 95 266 96 HOH HOH A . C 3 HOH 96 267 97 HOH HOH A . C 3 HOH 97 268 98 HOH HOH A . C 3 HOH 98 269 99 HOH HOH A . C 3 HOH 99 270 100 HOH HOH A . C 3 HOH 100 271 101 HOH HOH A . C 3 HOH 101 272 102 HOH HOH A . C 3 HOH 102 273 103 HOH HOH A . C 3 HOH 103 274 104 HOH HOH A . C 3 HOH 104 275 105 HOH HOH A . C 3 HOH 105 276 106 HOH HOH A . C 3 HOH 106 277 107 HOH HOH A . C 3 HOH 107 278 108 HOH HOH A . C 3 HOH 108 279 109 HOH HOH A . C 3 HOH 109 280 110 HOH HOH A . C 3 HOH 110 281 111 HOH HOH A . C 3 HOH 111 282 112 HOH HOH A . C 3 HOH 112 283 113 HOH HOH A . C 3 HOH 113 284 114 HOH HOH A . C 3 HOH 114 285 115 HOH HOH A . C 3 HOH 115 286 116 HOH HOH A . C 3 HOH 116 287 117 HOH HOH A . C 3 HOH 117 288 118 HOH HOH A . C 3 HOH 118 289 119 HOH HOH A . C 3 HOH 119 290 120 HOH HOH A . C 3 HOH 120 291 121 HOH HOH A . C 3 HOH 121 292 122 HOH HOH A . C 3 HOH 122 293 123 HOH HOH A . C 3 HOH 123 294 124 HOH HOH A . C 3 HOH 124 295 125 HOH HOH A . C 3 HOH 125 296 126 HOH HOH A . C 3 HOH 126 297 127 HOH HOH A . C 3 HOH 127 298 128 HOH HOH A . C 3 HOH 128 299 129 HOH HOH A . C 3 HOH 129 300 130 HOH HOH A . C 3 HOH 130 301 131 HOH HOH A . C 3 HOH 131 302 132 HOH HOH A . C 3 HOH 132 303 133 HOH HOH A . C 3 HOH 133 304 134 HOH HOH A . C 3 HOH 134 305 135 HOH HOH A . C 3 HOH 135 306 136 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 106 A MSE 105 ? MET SELENOMETHIONINE 2 A MSE 128 A MSE 127 ? MET SELENOMETHIONINE 3 A MSE 147 A MSE 146 ? MET SELENOMETHIONINE 4 A MSE 167 A MSE 166 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_prop.biol_id 1 _pdbx_struct_assembly_prop.type 'ABSA (A^2)' _pdbx_struct_assembly_prop.value 10210 _pdbx_struct_assembly_prop.details ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -18.6171452124 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 46.6169573561 # 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 2007-10-16 2 'Structure model' 1 1 2010-05-26 3 'Structure model' 1 2 2011-07-13 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 3 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # _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 MOLPROBITY 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu validation http://kinemage.biochem.duke.edu/molprobity/ ? ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHARP . ? package 'de La Fortelle' sharp-develop@globalphasing.com phasing http://babinet.globalphasing.com/sharp/ ? ? 3 REFMAC5 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 4 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data processing' 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 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 7 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 8 SCALA . ? ? ? ? 'data scaling' ? ? ? 9 SHELX . ? ? ? ? phasing ? ? ? 10 REFMAC 5.2.0019 ? ? ? ? refinement ? ? ? 11 # loop_ _pdbx_database_remark.id _pdbx_database_remark.text 300 ; BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. ; 999 ; SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. ; # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 N _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ASP _pdbx_validate_rmsd_angle.auth_seq_id_1 142 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CA _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ASP _pdbx_validate_rmsd_angle.auth_seq_id_2 142 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 C _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ASP _pdbx_validate_rmsd_angle.auth_seq_id_3 142 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 128.95 _pdbx_validate_rmsd_angle.angle_target_value 111.00 _pdbx_validate_rmsd_angle.angle_deviation 17.95 _pdbx_validate_rmsd_angle.angle_standard_deviation 2.70 _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 VAL A 45 ? ? -106.49 -64.02 2 1 GLU A 140 ? ? -109.54 70.54 3 1 SER A 141 ? ? -170.58 -167.87 4 1 ASP A 142 ? ? 85.25 -59.49 # _pdbx_validate_peptide_omega.id 1 _pdbx_validate_peptide_omega.PDB_model_num 1 _pdbx_validate_peptide_omega.auth_comp_id_1 SER _pdbx_validate_peptide_omega.auth_asym_id_1 A _pdbx_validate_peptide_omega.auth_seq_id_1 141 _pdbx_validate_peptide_omega.PDB_ins_code_1 ? _pdbx_validate_peptide_omega.label_alt_id_1 ? _pdbx_validate_peptide_omega.auth_comp_id_2 ASP _pdbx_validate_peptide_omega.auth_asym_id_2 A _pdbx_validate_peptide_omega.auth_seq_id_2 142 _pdbx_validate_peptide_omega.PDB_ins_code_2 ? _pdbx_validate_peptide_omega.label_alt_id_2 ? _pdbx_validate_peptide_omega.omega -56.06 # 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 2 ? CG ? A LYS 3 CG 2 1 Y 1 A LYS 2 ? CD ? A LYS 3 CD 3 1 Y 1 A LYS 2 ? CE ? A LYS 3 CE 4 1 Y 1 A LYS 2 ? NZ ? A LYS 3 NZ 5 1 Y 1 A GLN 72 ? OE1 ? A GLN 73 OE1 6 1 Y 1 A GLN 72 ? NE2 ? A GLN 73 NE2 7 1 Y 1 A LYS 76 ? CE ? A LYS 77 CE 8 1 Y 1 A LYS 76 ? NZ ? A LYS 77 NZ 9 1 Y 1 A LYS 79 ? NZ ? A LYS 80 NZ 10 1 Y 1 A GLU 140 ? CG ? A GLU 141 CG 11 1 Y 1 A GLU 140 ? CD ? A GLU 141 CD 12 1 Y 1 A GLU 140 ? OE1 ? A GLU 141 OE1 13 1 Y 1 A GLU 140 ? OE2 ? A GLU 141 OE2 14 1 Y 1 A SER 141 ? OG ? A SER 142 OG # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A MSE 1 ? A MSE 2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #