data_3HZP # _entry.id 3HZP # _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 3HZP pdb_00003hzp 10.2210/pdb3hzp/pdb RCSB RCSB053781 ? ? WWPDB D_1000053781 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 391203 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3HZP _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-06-24 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _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 NTF2-like protein of unknown function MN2A_0505 from Prochlorococcus marinus (YP_291699.1) from Prochlorococcus sp. NATL2A at 1.40 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 3HZP _cell.length_a 58.046 _cell.length_b 58.046 _cell.length_c 63.620 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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 3HZP _symmetry.Int_Tables_number 154 _symmetry.space_group_name_H-M 'P 32 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 'NTF2-like protein of unknown function' 14879.997 1 ? ? ? ? 2 non-polymer syn 'PENTAETHYLENE GLYCOL' 238.278 1 ? ? ? ? 3 water nat water 18.015 99 ? ? ? ? # _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)SSKEEILSILEAFASTER(MSE)GSFFLDNATADFLFIRPSGNPLDAKGFEN(MSE)WSSGDLVLESAEITKVH KFELLGSNAAICVFTLGSKFTYKGTQNDDLPTVTSIFKKIDEKWKVAW(MSE)QRSSGQSD(MSE)TLWNE ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSSKEEILSILEAFASTERMGSFFLDNATADFLFIRPSGNPLDAKGFENMWSSGDLVLESAEITKVHKFELLGSNAAIC VFTLGSKFTYKGTQNDDLPTVTSIFKKIDEKWKVAWMQRSSGQSDMTLWNE ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 391203 # 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 SER n 1 4 SER n 1 5 LYS n 1 6 GLU n 1 7 GLU n 1 8 ILE n 1 9 LEU n 1 10 SER n 1 11 ILE n 1 12 LEU n 1 13 GLU n 1 14 ALA n 1 15 PHE n 1 16 ALA n 1 17 SER n 1 18 THR n 1 19 GLU n 1 20 ARG n 1 21 MSE n 1 22 GLY n 1 23 SER n 1 24 PHE n 1 25 PHE n 1 26 LEU n 1 27 ASP n 1 28 ASN n 1 29 ALA n 1 30 THR n 1 31 ALA n 1 32 ASP n 1 33 PHE n 1 34 LEU n 1 35 PHE n 1 36 ILE n 1 37 ARG n 1 38 PRO n 1 39 SER n 1 40 GLY n 1 41 ASN n 1 42 PRO n 1 43 LEU n 1 44 ASP n 1 45 ALA n 1 46 LYS n 1 47 GLY n 1 48 PHE n 1 49 GLU n 1 50 ASN n 1 51 MSE n 1 52 TRP n 1 53 SER n 1 54 SER n 1 55 GLY n 1 56 ASP n 1 57 LEU n 1 58 VAL n 1 59 LEU n 1 60 GLU n 1 61 SER n 1 62 ALA n 1 63 GLU n 1 64 ILE n 1 65 THR n 1 66 LYS n 1 67 VAL n 1 68 HIS n 1 69 LYS n 1 70 PHE n 1 71 GLU n 1 72 LEU n 1 73 LEU n 1 74 GLY n 1 75 SER n 1 76 ASN n 1 77 ALA n 1 78 ALA n 1 79 ILE n 1 80 CYS n 1 81 VAL n 1 82 PHE n 1 83 THR n 1 84 LEU n 1 85 GLY n 1 86 SER n 1 87 LYS n 1 88 PHE n 1 89 THR n 1 90 TYR n 1 91 LYS n 1 92 GLY n 1 93 THR n 1 94 GLN n 1 95 ASN n 1 96 ASP n 1 97 ASP n 1 98 LEU n 1 99 PRO n 1 100 THR n 1 101 VAL n 1 102 THR n 1 103 SER n 1 104 ILE n 1 105 PHE n 1 106 LYS n 1 107 LYS n 1 108 ILE n 1 109 ASP n 1 110 GLU n 1 111 LYS n 1 112 TRP n 1 113 LYS n 1 114 VAL n 1 115 ALA n 1 116 TRP n 1 117 MSE n 1 118 GLN n 1 119 ARG n 1 120 SER n 1 121 SER n 1 122 GLY n 1 123 GLN n 1 124 SER n 1 125 ASP n 1 126 MSE n 1 127 THR n 1 128 LEU n 1 129 TRP n 1 130 ASN n 1 131 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 'PMN2A_0505, YP_291699.1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain NATL2A _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 'Prochlorococcus marinus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 59920 _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 Q46KI2_PROMT _struct_ref.pdbx_db_accession Q46KI2 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSSKEEILSILEAFASTERMGSFFLDNATADFLFIRPSGNPLDAKGFENMWSSGDLVLESAEITKVHKFELLGSNAAICV FTLGSKFTYKGTQNDDLPTVTSIFKKIDEKWKVAWMQRSSGQSDMTLWNE ; _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 3HZP _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 131 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q46KI2 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 130 _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 130 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3HZP _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 Q46KI2 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 1PE non-polymer . 'PENTAETHYLENE GLYCOL' PEG400 'C10 H22 O6' 238.278 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 3HZP # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.08 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 40.84 _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 5.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '40.0000% PEG-600, 0.1M Citrate pH 5.5, 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 CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat collimating mirror, toroid focusing mirror' _diffrn_detector.pdbx_collection_date 2009-03-18 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double crystal monochromator' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91162 1.0 2 0.97929 1.0 3 0.97918 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL9-2 _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list 0.91162,0.97929,0.97918 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3HZP _reflns.d_resolution_high 1.40 _reflns.d_resolution_low 29.025 _reflns.number_obs 24917 _reflns.pdbx_Rmerge_I_obs 0.075 _reflns.pdbx_netI_over_sigmaI 6.295 _reflns.pdbx_Rsym_value 0.075 _reflns.pdbx_redundancy 5.400 _reflns.percent_possible_obs 100.000 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate 14.990 _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 1.40 1.44 ? 9847 ? 0.748 1.0 0.748 ? 5.40 ? 1818 100.00 1 1 1.44 1.48 ? 9606 ? 0.597 1.3 0.597 ? 5.40 ? 1778 100.00 2 1 1.48 1.52 ? 9317 ? 0.451 1.7 0.451 ? 5.40 ? 1718 100.00 3 1 1.52 1.57 ? 9108 ? 0.383 2.0 0.383 ? 5.40 ? 1673 100.00 4 1 1.57 1.62 ? 8715 ? 0.315 2.4 0.315 ? 5.50 ? 1599 100.00 5 1 1.62 1.67 ? 8687 ? 0.253 3.0 0.253 ? 5.40 ? 1598 100.00 6 1 1.67 1.74 ? 8238 ? 0.210 3.6 0.210 ? 5.40 ? 1512 100.00 7 1 1.74 1.81 ? 7915 ? 0.174 4.3 0.174 ? 5.50 ? 1450 100.00 8 1 1.81 1.89 ? 7775 ? 0.133 5.6 0.133 ? 5.40 ? 1428 100.00 9 1 1.89 1.98 ? 7307 ? 0.103 7.1 0.103 ? 5.40 ? 1344 100.00 10 1 1.98 2.09 ? 6985 ? 0.089 7.7 0.089 ? 5.40 ? 1288 100.00 11 1 2.09 2.21 ? 6625 ? 0.085 7.9 0.085 ? 5.40 ? 1224 100.00 12 1 2.21 2.37 ? 6098 ? 0.078 8.5 0.078 ? 5.40 ? 1128 100.00 13 1 2.37 2.56 ? 5911 ? 0.067 9.6 0.067 ? 5.40 ? 1091 100.00 14 1 2.56 2.80 ? 5430 ? 0.060 10.5 0.060 ? 5.40 ? 1005 100.00 15 1 2.80 3.13 ? 4816 ? 0.056 11.4 0.056 ? 5.40 ? 893 100.00 16 1 3.13 3.61 ? 4361 ? 0.057 11.1 0.057 ? 5.40 ? 811 100.00 17 1 3.61 4.43 ? 3635 ? 0.044 13.6 0.044 ? 5.30 ? 687 100.00 18 1 4.43 6.26 ? 2825 ? 0.039 16.2 0.039 ? 5.10 ? 551 100.00 19 1 6.26 29.02 ? 1473 ? 0.045 14.2 0.045 ? 4.60 ? 321 98.50 20 1 # _refine.entry_id 3HZP _refine.ls_d_res_high 1.400 _refine.ls_d_res_low 29.025 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.980 _refine.ls_number_reflns_obs 24887 _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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULE(1PE) FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.168 _refine.ls_R_factor_R_work 0.167 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.184 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 1266 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 21.173 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.050 _refine.aniso_B[2][2] -0.050 _refine.aniso_B[3][3] 0.080 _refine.aniso_B[1][2] -0.030 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.969 _refine.correlation_coeff_Fo_to_Fc_free 0.964 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.061 _refine.pdbx_overall_ESU_R_Free 0.060 _refine.overall_SU_ML 0.039 _refine.overall_SU_B 2.111 _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.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 61.22 _refine.B_iso_min 8.35 _refine.occupancy_max 1.00 _refine.occupancy_min 0.25 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 990 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 16 _refine_hist.number_atoms_solvent 99 _refine_hist.number_atoms_total 1105 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 29.025 # loop_ _refine_ls_restr.type _refine_ls_restr.pdbx_refine_id _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 'X-RAY DIFFRACTION' 1179 0.017 0.022 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 789 0.001 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 1608 1.527 1.946 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 1947 0.785 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 160 6.813 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 47 35.135 25.532 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 204 13.043 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 2 13.242 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 173 0.085 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 1376 0.008 0.020 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 246 0.003 0.020 ? ? r_nbd_refined 'X-RAY DIFFRACTION' 215 0.222 0.300 ? ? r_nbd_other 'X-RAY DIFFRACTION' 842 0.203 0.300 ? ? r_nbtor_refined 'X-RAY DIFFRACTION' 589 0.192 0.500 ? ? r_nbtor_other 'X-RAY DIFFRACTION' 657 0.094 0.500 ? ? r_xyhbond_nbd_refined 'X-RAY DIFFRACTION' 146 0.246 0.500 ? ? r_symmetry_vdw_refined 'X-RAY DIFFRACTION' 19 0.274 0.300 ? ? r_symmetry_vdw_other 'X-RAY DIFFRACTION' 35 0.300 0.300 ? ? r_symmetry_hbond_refined 'X-RAY DIFFRACTION' 30 0.321 0.500 ? ? r_symmetry_hbond_other 'X-RAY DIFFRACTION' 1 0.381 0.500 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 765 2.034 3.000 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 296 0.460 3.000 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 1209 3.095 5.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 485 4.880 8.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 399 6.394 11.000 ? ? # _refine_ls_shell.d_res_high 1.400 _refine_ls_shell.d_res_low 1.436 _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 1731 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.239 _refine_ls_shell.R_factor_R_free 0.296 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 85 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1816 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3HZP _struct.title ;Crystal structure of NTF2-like protein of unknown function MN2A_0505 from Prochlorococcus marinus (YP_291699.1) from Prochlorococcus sp. NATL2A at 1.40 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;YP_291699.1, NTF2-like protein of unknown function MN2A_0505 from Prochlorococcus marinus, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function ; _struct_keywords.pdbx_keywords 'Structural Genomics, unknown function' _struct_keywords.entry_id 3HZP # 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 ;ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE DIMER IS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. ; # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 3 ? ALA A 16 ? SER A 2 ALA A 15 1 ? 14 HELX_P HELX_P2 2 SER A 23 ? ALA A 29 ? SER A 22 ALA A 28 1 ? 7 HELX_P HELX_P3 3 ASP A 44 ? SER A 53 ? ASP A 43 SER A 52 1 ? 10 HELX_P HELX_P4 4 ASP A 125 ? TRP A 129 ? ASP A 124 TRP A 128 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 MSE 2 C ? ? ? 1_555 A SER 3 N ? ? A MSE 1 A SER 2 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale2 covale both ? A ARG 20 C ? ? ? 1_555 A MSE 21 N ? ? A ARG 19 A MSE 20 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale3 covale both ? A MSE 21 C ? ? ? 1_555 A GLY 22 N ? ? A MSE 20 A GLY 21 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? A ASN 50 C ? ? ? 1_555 A MSE 51 N A ? A ASN 49 A MSE 50 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale5 covale both ? A ASN 50 C ? ? ? 1_555 A MSE 51 N B ? A ASN 49 A MSE 50 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale6 covale both ? A MSE 51 C A ? ? 1_555 A TRP 52 N ? ? A MSE 50 A TRP 51 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale7 covale both ? A MSE 51 C B ? ? 1_555 A TRP 52 N ? ? A MSE 50 A TRP 51 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale8 covale both ? A TRP 116 C ? ? ? 1_555 A MSE 117 N A ? A TRP 115 A MSE 116 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale9 covale both ? A TRP 116 C ? ? ? 1_555 A MSE 117 N B ? A TRP 115 A MSE 116 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale10 covale both ? A MSE 117 C A ? ? 1_555 A GLN 118 N ? ? A MSE 116 A GLN 117 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale11 covale both ? A MSE 117 C B ? ? 1_555 A GLN 118 N ? ? A MSE 116 A GLN 117 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale12 covale both ? A ASP 125 C ? ? ? 1_555 A MSE 126 N A ? A ASP 124 A MSE 125 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale13 covale both ? A ASP 125 C ? ? ? 1_555 A MSE 126 N B ? A ASP 124 A MSE 125 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale14 covale both ? A MSE 126 C A ? ? 1_555 A THR 127 N ? ? A MSE 125 A THR 126 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale15 covale both ? A MSE 126 C B ? ? 1_555 A THR 127 N ? ? A MSE 125 A THR 126 1_555 ? ? ? ? ? ? ? 1.332 ? ? # _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 ? 6 ? B ? 6 ? # 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 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? 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 PRO A 42 ? LEU A 43 ? PRO A 41 LEU A 42 A 2 PHE A 35 ? ILE A 36 ? PHE A 34 ILE A 35 A 3 LYS A 111 ? ARG A 119 ? LYS A 110 ARG A 118 A 4 THR A 100 ? ILE A 108 ? THR A 99 ILE A 107 A 5 ALA A 77 ? TYR A 90 ? ALA A 76 TYR A 89 A 6 LEU A 57 ? LEU A 72 ? LEU A 56 LEU A 71 B 1 PRO A 42 ? LEU A 43 ? PRO A 41 LEU A 42 B 2 PHE A 35 ? ILE A 36 ? PHE A 34 ILE A 35 B 3 LYS A 111 ? ARG A 119 ? LYS A 110 ARG A 118 B 4 THR A 100 ? ILE A 108 ? THR A 99 ILE A 107 B 5 ALA A 77 ? TYR A 90 ? ALA A 76 TYR A 89 B 6 THR A 93 ? ASP A 97 ? THR A 92 ASP A 96 # 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 O LEU A 43 ? O LEU A 42 N PHE A 35 ? N PHE A 34 A 2 3 N ILE A 36 ? N ILE A 35 O MSE A 117 ? O MSE A 116 A 3 4 O ALA A 115 ? O ALA A 114 N ILE A 104 ? N ILE A 103 A 4 5 O VAL A 101 ? O VAL A 100 N PHE A 82 ? N PHE A 81 A 5 6 O THR A 89 ? O THR A 88 N VAL A 58 ? N VAL A 57 B 1 2 O LEU A 43 ? O LEU A 42 N PHE A 35 ? N PHE A 34 B 2 3 N ILE A 36 ? N ILE A 35 O MSE A 117 ? O MSE A 116 B 3 4 O ALA A 115 ? O ALA A 114 N ILE A 104 ? N ILE A 103 B 4 5 O VAL A 101 ? O VAL A 100 N PHE A 82 ? N PHE A 81 B 5 6 N PHE A 88 ? N PHE A 87 O ASN A 95 ? O ASN A 94 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id 1PE _struct_site.pdbx_auth_seq_id 131 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 7 _struct_site.details 'BINDING SITE FOR RESIDUE 1PE A 131' # 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 7 PHE A 35 ? PHE A 34 . ? 1_555 ? 2 AC1 7 TRP A 52 ? TRP A 51 . ? 1_555 ? 3 AC1 7 LEU A 84 ? LEU A 83 . ? 1_555 ? 4 AC1 7 PHE A 88 ? PHE A 87 . ? 1_555 ? 5 AC1 7 ARG A 119 ? ARG A 118 . ? 1_555 ? 6 AC1 7 HOH C . ? HOH A 206 . ? 1_555 ? 7 AC1 7 HOH C . ? HOH A 217 . ? 1_555 ? # _atom_sites.entry_id 3HZP _atom_sites.fract_transf_matrix[1][1] 0.017228 _atom_sites.fract_transf_matrix[1][2] 0.009946 _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] 0.019893 _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] 0.015718 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 SER 3 2 2 SER SER A . n A 1 4 SER 4 3 3 SER SER A . n A 1 5 LYS 5 4 4 LYS LYS A . n A 1 6 GLU 6 5 5 GLU GLU A . n A 1 7 GLU 7 6 6 GLU GLU A . n A 1 8 ILE 8 7 7 ILE ILE A . n A 1 9 LEU 9 8 8 LEU LEU A . n A 1 10 SER 10 9 9 SER SER A . n A 1 11 ILE 11 10 10 ILE ILE A . n A 1 12 LEU 12 11 11 LEU LEU A . n A 1 13 GLU 13 12 12 GLU GLU A . n A 1 14 ALA 14 13 13 ALA ALA A . n A 1 15 PHE 15 14 14 PHE PHE A . n A 1 16 ALA 16 15 15 ALA ALA A . n A 1 17 SER 17 16 16 SER SER A . n A 1 18 THR 18 17 17 THR THR A . n A 1 19 GLU 19 18 18 GLU GLU A . n A 1 20 ARG 20 19 19 ARG ARG A . n A 1 21 MSE 21 20 20 MSE MSE A . n A 1 22 GLY 22 21 21 GLY GLY A . n A 1 23 SER 23 22 22 SER SER A . n A 1 24 PHE 24 23 23 PHE PHE A . n A 1 25 PHE 25 24 24 PHE PHE A . n A 1 26 LEU 26 25 25 LEU LEU A . n A 1 27 ASP 27 26 26 ASP ASP A . n A 1 28 ASN 28 27 27 ASN ASN A . n A 1 29 ALA 29 28 28 ALA ALA A . n A 1 30 THR 30 29 29 THR THR A . n A 1 31 ALA 31 30 30 ALA ALA A . n A 1 32 ASP 32 31 31 ASP ASP A . n A 1 33 PHE 33 32 32 PHE PHE A . n A 1 34 LEU 34 33 33 LEU LEU A . n A 1 35 PHE 35 34 34 PHE PHE A . n A 1 36 ILE 36 35 35 ILE ILE A . n A 1 37 ARG 37 36 36 ARG ARG A . n A 1 38 PRO 38 37 37 PRO PRO A . n A 1 39 SER 39 38 38 SER SER A . n A 1 40 GLY 40 39 39 GLY GLY A . n A 1 41 ASN 41 40 40 ASN ASN A . n A 1 42 PRO 42 41 41 PRO PRO A . n A 1 43 LEU 43 42 42 LEU LEU A . n A 1 44 ASP 44 43 43 ASP ASP A . n A 1 45 ALA 45 44 44 ALA ALA A . n A 1 46 LYS 46 45 45 LYS LYS A . n A 1 47 GLY 47 46 46 GLY GLY A . n A 1 48 PHE 48 47 47 PHE PHE A . n A 1 49 GLU 49 48 48 GLU GLU A . n A 1 50 ASN 50 49 49 ASN ASN A . n A 1 51 MSE 51 50 50 MSE MSE A . n A 1 52 TRP 52 51 51 TRP TRP 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 GLY 55 54 54 GLY GLY A . n A 1 56 ASP 56 55 55 ASP ASP A . n A 1 57 LEU 57 56 56 LEU LEU A . n A 1 58 VAL 58 57 57 VAL VAL A . n A 1 59 LEU 59 58 58 LEU LEU A . n A 1 60 GLU 60 59 59 GLU GLU A . n A 1 61 SER 61 60 60 SER SER A . n A 1 62 ALA 62 61 61 ALA ALA A . n A 1 63 GLU 63 62 62 GLU GLU A . n A 1 64 ILE 64 63 63 ILE ILE A . n A 1 65 THR 65 64 64 THR THR A . n A 1 66 LYS 66 65 65 LYS LYS A . n A 1 67 VAL 67 66 66 VAL VAL A . n A 1 68 HIS 68 67 67 HIS HIS A . n A 1 69 LYS 69 68 68 LYS LYS A . n A 1 70 PHE 70 69 69 PHE PHE A . n A 1 71 GLU 71 70 70 GLU GLU A . n A 1 72 LEU 72 71 71 LEU LEU A . n A 1 73 LEU 73 72 72 LEU LEU A . n A 1 74 GLY 74 73 73 GLY GLY A . n A 1 75 SER 75 74 74 SER SER A . n A 1 76 ASN 76 75 75 ASN ASN A . n A 1 77 ALA 77 76 76 ALA ALA A . n A 1 78 ALA 78 77 77 ALA ALA A . n A 1 79 ILE 79 78 78 ILE ILE A . n A 1 80 CYS 80 79 79 CYS CYS A . n A 1 81 VAL 81 80 80 VAL VAL A . n A 1 82 PHE 82 81 81 PHE PHE A . n A 1 83 THR 83 82 82 THR THR A . n A 1 84 LEU 84 83 83 LEU LEU A . n A 1 85 GLY 85 84 84 GLY GLY A . n A 1 86 SER 86 85 85 SER SER A . n A 1 87 LYS 87 86 86 LYS LYS A . n A 1 88 PHE 88 87 87 PHE PHE A . n A 1 89 THR 89 88 88 THR THR A . n A 1 90 TYR 90 89 89 TYR TYR A . n A 1 91 LYS 91 90 90 LYS LYS A . n A 1 92 GLY 92 91 91 GLY GLY A . n A 1 93 THR 93 92 92 THR THR A . n A 1 94 GLN 94 93 93 GLN GLN A . n A 1 95 ASN 95 94 94 ASN ASN A . n A 1 96 ASP 96 95 95 ASP ASP A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 LEU 98 97 97 LEU LEU A . n A 1 99 PRO 99 98 98 PRO PRO A . n A 1 100 THR 100 99 99 THR THR A . n A 1 101 VAL 101 100 100 VAL VAL A . n A 1 102 THR 102 101 101 THR THR A . n A 1 103 SER 103 102 102 SER SER A . n A 1 104 ILE 104 103 103 ILE ILE A . n A 1 105 PHE 105 104 104 PHE PHE A . n A 1 106 LYS 106 105 105 LYS LYS A . n A 1 107 LYS 107 106 106 LYS LYS A . n A 1 108 ILE 108 107 107 ILE ILE A . n A 1 109 ASP 109 108 108 ASP ASP A . n A 1 110 GLU 110 109 109 GLU GLU A . n A 1 111 LYS 111 110 110 LYS LYS A . n A 1 112 TRP 112 111 111 TRP TRP A . n A 1 113 LYS 113 112 112 LYS LYS A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 ALA 115 114 114 ALA ALA A . n A 1 116 TRP 116 115 115 TRP TRP A . n A 1 117 MSE 117 116 116 MSE MSE A . n A 1 118 GLN 118 117 117 GLN GLN A . n A 1 119 ARG 119 118 118 ARG ARG A . n A 1 120 SER 120 119 119 SER SER A . n A 1 121 SER 121 120 120 SER SER A . n A 1 122 GLY 122 121 121 GLY GLY A . n A 1 123 GLN 123 122 122 GLN GLN A . n A 1 124 SER 124 123 123 SER SER A . n A 1 125 ASP 125 124 124 ASP ASP A . n A 1 126 MSE 126 125 125 MSE MSE A . n A 1 127 THR 127 126 126 THR THR A . n A 1 128 LEU 128 127 127 LEU LEU A . n A 1 129 TRP 129 128 128 TRP TRP A . n A 1 130 ASN 130 129 ? ? ? A . n A 1 131 GLU 131 130 ? ? ? 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 1PE 1 131 1 1PE 1PE A . C 3 HOH 1 132 2 HOH HOH A . C 3 HOH 2 133 3 HOH HOH A . C 3 HOH 3 134 4 HOH HOH A . C 3 HOH 4 135 5 HOH HOH A . C 3 HOH 5 136 6 HOH HOH A . C 3 HOH 6 137 7 HOH HOH A . C 3 HOH 7 138 8 HOH HOH A . C 3 HOH 8 139 9 HOH HOH A . C 3 HOH 9 140 10 HOH HOH A . C 3 HOH 10 141 11 HOH HOH A . C 3 HOH 11 142 12 HOH HOH A . C 3 HOH 12 143 13 HOH HOH A . C 3 HOH 13 144 14 HOH HOH A . C 3 HOH 14 145 15 HOH HOH A . C 3 HOH 15 146 16 HOH HOH A . C 3 HOH 16 147 17 HOH HOH A . C 3 HOH 17 148 18 HOH HOH A . C 3 HOH 18 149 19 HOH HOH A . C 3 HOH 19 150 20 HOH HOH A . C 3 HOH 20 151 21 HOH HOH A . C 3 HOH 21 152 22 HOH HOH A . C 3 HOH 22 153 23 HOH HOH A . C 3 HOH 23 154 24 HOH HOH A . C 3 HOH 24 155 25 HOH HOH A . C 3 HOH 25 156 26 HOH HOH A . C 3 HOH 26 157 27 HOH HOH A . C 3 HOH 27 158 28 HOH HOH A . C 3 HOH 28 159 29 HOH HOH A . C 3 HOH 29 160 30 HOH HOH A . C 3 HOH 30 161 31 HOH HOH A . C 3 HOH 31 162 32 HOH HOH A . C 3 HOH 32 163 33 HOH HOH A . C 3 HOH 33 164 34 HOH HOH A . C 3 HOH 34 165 35 HOH HOH A . C 3 HOH 35 166 36 HOH HOH A . C 3 HOH 36 167 37 HOH HOH A . C 3 HOH 37 168 38 HOH HOH A . C 3 HOH 38 169 39 HOH HOH A . C 3 HOH 39 170 40 HOH HOH A . C 3 HOH 40 171 41 HOH HOH A . C 3 HOH 41 172 42 HOH HOH A . C 3 HOH 42 173 43 HOH HOH A . C 3 HOH 43 174 44 HOH HOH A . C 3 HOH 44 175 45 HOH HOH A . C 3 HOH 45 176 46 HOH HOH A . C 3 HOH 46 177 47 HOH HOH A . C 3 HOH 47 178 48 HOH HOH A . C 3 HOH 48 179 49 HOH HOH A . C 3 HOH 49 180 50 HOH HOH A . C 3 HOH 50 181 51 HOH HOH A . C 3 HOH 51 182 52 HOH HOH A . C 3 HOH 52 183 53 HOH HOH A . C 3 HOH 53 184 54 HOH HOH A . C 3 HOH 54 185 55 HOH HOH A . C 3 HOH 55 186 56 HOH HOH A . C 3 HOH 56 187 57 HOH HOH A . C 3 HOH 57 188 58 HOH HOH A . C 3 HOH 58 189 59 HOH HOH A . C 3 HOH 59 190 60 HOH HOH A . C 3 HOH 60 191 61 HOH HOH A . C 3 HOH 61 192 62 HOH HOH A . C 3 HOH 62 193 63 HOH HOH A . C 3 HOH 63 194 64 HOH HOH A . C 3 HOH 64 195 65 HOH HOH A . C 3 HOH 65 196 66 HOH HOH A . C 3 HOH 66 197 67 HOH HOH A . C 3 HOH 67 198 68 HOH HOH A . C 3 HOH 68 199 69 HOH HOH A . C 3 HOH 69 200 70 HOH HOH A . C 3 HOH 70 201 71 HOH HOH A . C 3 HOH 71 202 72 HOH HOH A . C 3 HOH 72 203 73 HOH HOH A . C 3 HOH 73 204 74 HOH HOH A . C 3 HOH 74 205 75 HOH HOH A . C 3 HOH 75 206 76 HOH HOH A . C 3 HOH 76 207 77 HOH HOH A . C 3 HOH 77 208 78 HOH HOH A . C 3 HOH 78 209 79 HOH HOH A . C 3 HOH 79 210 80 HOH HOH A . C 3 HOH 80 211 81 HOH HOH A . C 3 HOH 81 212 82 HOH HOH A . C 3 HOH 82 213 83 HOH HOH A . C 3 HOH 83 214 84 HOH HOH A . C 3 HOH 84 215 85 HOH HOH A . C 3 HOH 85 216 86 HOH HOH A . C 3 HOH 86 217 87 HOH HOH A . C 3 HOH 87 218 88 HOH HOH A . C 3 HOH 88 219 89 HOH HOH A . C 3 HOH 89 220 90 HOH HOH A . C 3 HOH 90 221 91 HOH HOH A . C 3 HOH 91 222 92 HOH HOH A . C 3 HOH 92 223 93 HOH HOH A . C 3 HOH 93 224 94 HOH HOH A . C 3 HOH 94 225 95 HOH HOH A . C 3 HOH 95 226 96 HOH HOH A . C 3 HOH 96 227 97 HOH HOH A . C 3 HOH 97 228 98 HOH HOH A . C 3 HOH 98 229 99 HOH HOH A . C 3 HOH 99 230 100 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 21 A MSE 20 ? MET SELENOMETHIONINE 3 A MSE 51 A MSE 50 ? MET SELENOMETHIONINE 4 A MSE 117 A MSE 116 ? MET SELENOMETHIONINE 5 A MSE 126 A MSE 125 ? 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 # 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)' 3390 ? 1 MORE -20 ? 1 'SSA (A^2)' 11380 ? # 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' 5_555 x-y,-y,-z+1/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 21.2066666667 # 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 HOH 132 ? C HOH . 2 1 A HOH 140 ? C HOH . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2009-07-07 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' 'Author supporting evidence' 5 3 'Structure model' 'Refinement description' 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Derived calculations' 8 4 'Structure model' 'Refinement description' 9 5 'Structure model' 'Database references' 10 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' pdbx_struct_assembly_auth_evidence 2 3 'Structure model' software 3 4 'Structure model' pdbx_struct_special_symmetry 4 4 'Structure model' software 5 4 'Structure model' struct_conn 6 5 'Structure model' database_2 7 5 'Structure model' struct_ref_seq_dif 8 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_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.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 38.3963 _pdbx_refine_tls.origin_y 10.3180 _pdbx_refine_tls.origin_z 7.3702 _pdbx_refine_tls.T[1][1] -0.0087 _pdbx_refine_tls.T[2][2] -0.0293 _pdbx_refine_tls.T[3][3] -0.0237 _pdbx_refine_tls.T[1][2] -0.0001 _pdbx_refine_tls.T[1][3] -0.0080 _pdbx_refine_tls.T[2][3] -0.0057 _pdbx_refine_tls.L[1][1] 0.8158 _pdbx_refine_tls.L[2][2] 0.7225 _pdbx_refine_tls.L[3][3] 0.5845 _pdbx_refine_tls.L[1][2] 0.1870 _pdbx_refine_tls.L[1][3] -0.2987 _pdbx_refine_tls.L[2][3] -0.2403 _pdbx_refine_tls.S[1][1] -0.0265 _pdbx_refine_tls.S[2][2] 0.0313 _pdbx_refine_tls.S[3][3] -0.0048 _pdbx_refine_tls.S[1][2] -0.0042 _pdbx_refine_tls.S[1][3] 0.1099 _pdbx_refine_tls.S[2][3] -0.0096 _pdbx_refine_tls.S[2][1] 0.0191 _pdbx_refine_tls.S[3][1] -0.0517 _pdbx_refine_tls.S[3][2] -0.0031 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 128 _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # _phasing.method MAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.2.0019 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SOLVE . ? program 'Tom Terwilliger' terwilliger@LANL.gov phasing http://www.solve.lanl.gov/ ? ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 SCALA 3.2.5 5/04/2004 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 5 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 7 # _pdbx_entry_details.entry_id 3HZP _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 N _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 SER _pdbx_validate_symm_contact.auth_seq_id_1 3 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OE1 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 GLU _pdbx_validate_symm_contact.auth_seq_id_2 59 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 B _pdbx_validate_symm_contact.site_symmetry_2 4_545 _pdbx_validate_symm_contact.dist 2.02 # 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 GLU 5 ? CD ? A GLU 6 CD 2 1 Y 1 A GLU 5 ? OE1 ? A GLU 6 OE1 3 1 Y 1 A GLU 5 ? OE2 ? A GLU 6 OE2 4 1 Y 1 A LEU 8 ? CD1 ? A LEU 9 CD1 5 1 Y 1 A LEU 8 ? CD2 ? A LEU 9 CD2 6 1 Y 1 A ARG 19 ? NE ? A ARG 20 NE 7 1 Y 1 A ARG 19 ? CZ ? A ARG 20 CZ 8 1 Y 1 A ARG 19 ? NH1 ? A ARG 20 NH1 9 1 Y 1 A ARG 19 ? NH2 ? A ARG 20 NH2 10 1 Y 1 A LYS 45 ? CE ? A LYS 46 CE 11 1 Y 1 A LYS 45 ? NZ ? A LYS 46 NZ 12 1 Y 1 A LYS 90 ? CG ? A LYS 91 CG 13 1 Y 1 A LYS 90 ? CD ? A LYS 91 CD 14 1 Y 1 A LYS 90 ? CE ? A LYS 91 CE 15 1 Y 1 A LYS 90 ? NZ ? A LYS 91 NZ 16 1 Y 1 A LYS 110 ? CE ? A LYS 111 CE 17 1 Y 1 A LYS 110 ? NZ ? A LYS 111 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A ASN 129 ? A ASN 130 3 1 Y 1 A GLU 130 ? A GLU 131 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PENTAETHYLENE GLYCOL' 1PE 3 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #