data_4NJY # _entry.id 4NJY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.325 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4NJY RCSB RCSB083297 WWPDB D_1000083297 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2020-04-29 _pdbx_database_PDB_obs_spr.pdb_id 6YPR _pdbx_database_PDB_obs_spr.replace_pdb_id 4NJY _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NJX 'The same protein crystallized in P41212 space group' unspecified PDB 4NJZ . unspecified PDB 4NK0 . unspecified # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 4NJY _pdbx_database_status.recvd_initial_deposition_date 2013-11-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dolot, R.M.' 1 'Wlodarczyk, A.' 2 'Bujacz, G.D.' 3 'Nawrot, B.' 4 # _citation.id primary _citation.title 'Human histidine triad nucleotide-binding protein 2 (hHINT2) in H32 space group at 1.32 A' _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 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dolot, R.M.' 1 ? primary 'Wlodarczyk, A.' 2 ? primary 'Bujacz, G.D.' 3 ? primary 'Nawrot, B.' 4 ? # _cell.entry_id 4NJY _cell.length_a 71.733 _cell.length_b 71.733 _cell.length_c 102.527 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? _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 4NJY _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _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 'Histidine triad nucleotide-binding protein 2, mitochondrial' 17183.725 1 3.-.-.- ? ? ? 2 non-polymer syn 'PHOSPHATE ION' 94.971 1 ? ? ? ? 3 water nat water 18.015 192 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'HINT-2, HINT-3, HIT-17kDa, PKCI-1-related HIT protein' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MAAAVVLAAGLRAARRAVAATGVRGGQVRGAAGVTDGNEVAKAQQATPGGAAPTIFSRILDKSLPADILYEDQQCLVFRD VAPQAPVHFLVIPKKPIPRISQAEEEDQQLLGHLLLVAKQTAKAEGLGDGYRLVINDGKLGAQSVYHLHIHVLGGRQLQW PPG ; _entity_poly.pdbx_seq_one_letter_code_can ;MAAAVVLAAGLRAARRAVAATGVRGGQVRGAAGVTDGNEVAKAQQATPGGAAPTIFSRILDKSLPADILYEDQQCLVFRD VAPQAPVHFLVIPKKPIPRISQAEEEDQQLLGHLLLVAKQTAKAEGLGDGYRLVINDGKLGAQSVYHLHIHVLGGRQLQW PPG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ALA n 1 3 ALA n 1 4 ALA n 1 5 VAL n 1 6 VAL n 1 7 LEU n 1 8 ALA n 1 9 ALA n 1 10 GLY n 1 11 LEU n 1 12 ARG n 1 13 ALA n 1 14 ALA n 1 15 ARG n 1 16 ARG n 1 17 ALA n 1 18 VAL n 1 19 ALA n 1 20 ALA n 1 21 THR n 1 22 GLY n 1 23 VAL n 1 24 ARG n 1 25 GLY n 1 26 GLY n 1 27 GLN n 1 28 VAL n 1 29 ARG n 1 30 GLY n 1 31 ALA n 1 32 ALA n 1 33 GLY n 1 34 VAL n 1 35 THR n 1 36 ASP n 1 37 GLY n 1 38 ASN n 1 39 GLU n 1 40 VAL n 1 41 ALA n 1 42 LYS n 1 43 ALA n 1 44 GLN n 1 45 GLN n 1 46 ALA n 1 47 THR n 1 48 PRO n 1 49 GLY n 1 50 GLY n 1 51 ALA n 1 52 ALA n 1 53 PRO n 1 54 THR n 1 55 ILE n 1 56 PHE n 1 57 SER n 1 58 ARG n 1 59 ILE n 1 60 LEU n 1 61 ASP n 1 62 LYS n 1 63 SER n 1 64 LEU n 1 65 PRO n 1 66 ALA n 1 67 ASP n 1 68 ILE n 1 69 LEU n 1 70 TYR n 1 71 GLU n 1 72 ASP n 1 73 GLN n 1 74 GLN n 1 75 CYS n 1 76 LEU n 1 77 VAL n 1 78 PHE n 1 79 ARG n 1 80 ASP n 1 81 VAL n 1 82 ALA n 1 83 PRO n 1 84 GLN n 1 85 ALA n 1 86 PRO n 1 87 VAL n 1 88 HIS n 1 89 PHE n 1 90 LEU n 1 91 VAL n 1 92 ILE n 1 93 PRO n 1 94 LYS n 1 95 LYS n 1 96 PRO n 1 97 ILE n 1 98 PRO n 1 99 ARG n 1 100 ILE n 1 101 SER n 1 102 GLN n 1 103 ALA n 1 104 GLU n 1 105 GLU n 1 106 GLU n 1 107 ASP n 1 108 GLN n 1 109 GLN n 1 110 LEU n 1 111 LEU n 1 112 GLY n 1 113 HIS n 1 114 LEU n 1 115 LEU n 1 116 LEU n 1 117 VAL n 1 118 ALA n 1 119 LYS n 1 120 GLN n 1 121 THR n 1 122 ALA n 1 123 LYS n 1 124 ALA n 1 125 GLU n 1 126 GLY n 1 127 LEU n 1 128 GLY n 1 129 ASP n 1 130 GLY n 1 131 TYR n 1 132 ARG n 1 133 LEU n 1 134 VAL n 1 135 ILE n 1 136 ASN n 1 137 ASP n 1 138 GLY n 1 139 LYS n 1 140 LEU n 1 141 GLY n 1 142 ALA n 1 143 GLN n 1 144 SER n 1 145 VAL n 1 146 TYR n 1 147 HIS n 1 148 LEU n 1 149 HIS n 1 150 ILE n 1 151 HIS n 1 152 VAL n 1 153 LEU n 1 154 GLY n 1 155 GLY n 1 156 ARG n 1 157 GLN n 1 158 LEU n 1 159 GLN n 1 160 TRP n 1 161 PRO n 1 162 PRO n 1 163 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene HINT2 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 469008 _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 'BL21 DE3' _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 pGAT2 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code HINT2_HUMAN _struct_ref.pdbx_db_accession Q9BX68 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MAAAVVLAAGLRAARRAVAATGVRGGQVRGAAGVTDGNEVAKAQQATPGGAAPTIFSRILDKSLPADILYEDQQCLVFRD VAPQAPVHFLVIPKKPIPRISQAEEEDQQLLGHLLLVAKQTAKAEGLGDGYRLVINDGKLGAQSVYHLHIHVLGGRQLQW PPG ; _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 4NJY _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 163 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9BX68 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 163 _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 163 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PO4 non-polymer . 'PHOSPHATE ION' ? 'O4 P -3' 94.971 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4NJY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.48 _exptl_crystal.density_percent_sol 16.73 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 278 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '14% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2013-07-29 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si (111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9669 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)' _diffrn_source.pdbx_synchrotron_site 'PETRA III, EMBL c/o DESY' _diffrn_source.pdbx_synchrotron_beamline 'P13 (MX1)' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9669 # _reflns.entry_id 4NJY _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F 3.0 _reflns.d_resolution_low 53.131 _reflns.d_resolution_high 1.32 _reflns.number_obs 467633 _reflns.number_all 467633 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.061 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 29.4 _reflns.B_iso_Wilson_estimate 11.1 _reflns.pdbx_redundancy 19.4 _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 # _reflns_shell.d_res_high 1.32 _reflns_shell.d_res_low 1.34 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.947 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.4 _reflns_shell.pdbx_redundancy 19.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1271 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4NJY _refine.ls_number_reflns_obs 22863 _refine.ls_number_reflns_all 24100 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 53.13 _refine.ls_d_res_high 1.32 _refine.ls_percent_reflns_obs 99.98 _refine.ls_R_factor_obs 0.13857 _refine.ls_R_factor_all 0.13857 _refine.ls_R_factor_R_work 0.13732 _refine.ls_R_factor_R_free 0.16382 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 1231 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.979 _refine.correlation_coeff_Fo_to_Fc_free 0.974 _refine.B_iso_mean 19.719 _refine.aniso_B[1][1] 0.24 _refine.aniso_B[2][2] 0.24 _refine.aniso_B[3][3] -0.77 _refine.aniso_B[1][2] 0.12 _refine.aniso_B[1][3] -0.00 _refine.aniso_B[2][3] -0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'PDB ENTRY 3TW2' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.046 _refine.pdbx_overall_ESU_R_Free 0.049 _refine.overall_SU_ML 0.034 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 0.816 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 774 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 192 _refine_hist.number_atoms_total 971 _refine_hist.d_res_high 1.32 _refine_hist.d_res_low 53.13 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.025 0.019 ? 975 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.002 0.020 ? 953 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 2.464 1.973 ? 1346 ? 'X-RAY DIFFRACTION' r_angle_other_deg 0.969 3.000 ? 2200 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 7.140 5.000 ? 131 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 44.088 24.792 ? 48 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 11.712 15.000 ? 172 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 12.131 15.000 ? 6 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.151 0.200 ? 140 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.013 0.021 ? 1201 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.002 0.020 ? 237 ? 'X-RAY DIFFRACTION' r_mcbond_it 2.124 1.523 ? 482 ? 'X-RAY DIFFRACTION' r_mcbond_other 2.123 1.522 ? 481 ? 'X-RAY DIFFRACTION' r_mcangle_it 2.723 2.272 ? 627 ? 'X-RAY DIFFRACTION' r_mcangle_other 2.721 2.272 ? 628 ? 'X-RAY DIFFRACTION' r_scbond_it 3.196 1.865 ? 493 ? 'X-RAY DIFFRACTION' r_scbond_other 3.113 1.859 ? 489 ? 'X-RAY DIFFRACTION' r_scangle_other 4.925 2.672 ? 713 ? 'X-RAY DIFFRACTION' r_long_range_B_refined 8.489 16.644 ? 1283 ? 'X-RAY DIFFRACTION' r_long_range_B_other 7.784 13.828 ? 1138 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.320 _refine_ls_shell.d_res_low 1.354 _refine_ls_shell.number_reflns_R_work 1673 _refine_ls_shell.R_factor_R_work 0.205 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.232 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 99 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4NJY _struct.title 'Human histidine triad nucleotide-binding protein 2 (hHINT2) in H32 space group at 1.32 A' _struct.pdbx_descriptor 'Histidine triad nucleotide-binding protein 2, mitochondrial (E.C.3.-.-.-)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NJY _struct_keywords.pdbx_keywords 'Hydrolase, dna binding protein' _struct_keywords.text 'HINT, histidine triad, HIT, phosphoramidase, Hydrolase, dna binding protein' # 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 ? # 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 ARG A 99 ? ALA A 103 ? ARG A 99 ALA A 103 5 ? 5 HELX_P HELX_P2 2 GLU A 104 ? GLU A 106 ? GLU A 104 GLU A 106 5 ? 3 HELX_P HELX_P3 3 ASP A 107 ? GLU A 125 ? ASP A 107 GLU A 125 1 ? 19 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id TRP _struct_mon_prot_cis.label_seq_id 160 _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 TRP _struct_mon_prot_cis.auth_seq_id 160 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 161 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 161 _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 17.11 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ILE A 68 ? GLU A 71 ? ILE A 68 GLU A 71 A 2 CYS A 75 ? ARG A 79 ? CYS A 75 ARG A 79 A 3 VAL A 87 ? PRO A 93 ? VAL A 87 PRO A 93 A 4 ILE A 150 ? GLY A 154 ? ILE A 150 GLY A 154 A 5 TYR A 131 ? VAL A 134 ? TYR A 131 VAL A 134 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N TYR A 70 ? N TYR A 70 O VAL A 77 ? O VAL A 77 A 2 3 N PHE A 78 ? N PHE A 78 O LEU A 90 ? O LEU A 90 A 3 4 N PHE A 89 ? N PHE A 89 O VAL A 152 ? O VAL A 152 A 4 5 O HIS A 151 ? O HIS A 151 N VAL A 134 ? N VAL A 134 # _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 10 _struct_site.details 'BINDING SITE FOR RESIDUE PO4 A 201' # 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 10 ASN A 136 ? ASN A 136 . ? 1_555 ? 2 AC1 10 ALA A 142 ? ALA A 142 . ? 1_555 ? 3 AC1 10 GLN A 143 ? GLN A 143 . ? 1_555 ? 4 AC1 10 SER A 144 ? SER A 144 . ? 1_555 ? 5 AC1 10 VAL A 145 ? VAL A 145 . ? 1_555 ? 6 AC1 10 HIS A 149 ? HIS A 149 . ? 1_555 ? 7 AC1 10 HIS A 151 ? HIS A 151 . ? 1_555 ? 8 AC1 10 HOH C . ? HOH A 301 . ? 1_555 ? 9 AC1 10 HOH C . ? HOH A 302 . ? 1_555 ? 10 AC1 10 HOH C . ? HOH A 419 . ? 1_555 ? # _database_PDB_matrix.entry_id 4NJY _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4NJY _atom_sites.fract_transf_matrix[1][1] 0.013941 _atom_sites.fract_transf_matrix[1][2] 0.008049 _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] 0.016097 _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] 0.009754 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # 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 MET 1 1 ? ? ? A . n A 1 2 ALA 2 2 ? ? ? A . n A 1 3 ALA 3 3 ? ? ? A . n A 1 4 ALA 4 4 ? ? ? A . n A 1 5 VAL 5 5 ? ? ? A . n A 1 6 VAL 6 6 ? ? ? A . n A 1 7 LEU 7 7 ? ? ? A . n A 1 8 ALA 8 8 ? ? ? A . n A 1 9 ALA 9 9 ? ? ? A . n A 1 10 GLY 10 10 ? ? ? A . n A 1 11 LEU 11 11 ? ? ? A . n A 1 12 ARG 12 12 ? ? ? A . n A 1 13 ALA 13 13 ? ? ? A . n A 1 14 ALA 14 14 ? ? ? A . n A 1 15 ARG 15 15 ? ? ? A . n A 1 16 ARG 16 16 ? ? ? A . n A 1 17 ALA 17 17 ? ? ? A . n A 1 18 VAL 18 18 ? ? ? A . n A 1 19 ALA 19 19 ? ? ? A . n A 1 20 ALA 20 20 ? ? ? A . n A 1 21 THR 21 21 ? ? ? A . n A 1 22 GLY 22 22 ? ? ? A . n A 1 23 VAL 23 23 ? ? ? A . n A 1 24 ARG 24 24 ? ? ? A . n A 1 25 GLY 25 25 ? ? ? A . n A 1 26 GLY 26 26 ? ? ? A . n A 1 27 GLN 27 27 ? ? ? A . n A 1 28 VAL 28 28 ? ? ? A . n A 1 29 ARG 29 29 ? ? ? A . n A 1 30 GLY 30 30 ? ? ? A . n A 1 31 ALA 31 31 ? ? ? A . n A 1 32 ALA 32 32 ? ? ? A . n A 1 33 GLY 33 33 ? ? ? A . n A 1 34 VAL 34 34 ? ? ? A . n A 1 35 THR 35 35 ? ? ? A . n A 1 36 ASP 36 36 ? ? ? A . n A 1 37 GLY 37 37 ? ? ? A . n A 1 38 ASN 38 38 ? ? ? A . n A 1 39 GLU 39 39 ? ? ? A . n A 1 40 VAL 40 40 ? ? ? A . n A 1 41 ALA 41 41 ? ? ? A . n A 1 42 LYS 42 42 ? ? ? A . n A 1 43 ALA 43 43 ? ? ? A . n A 1 44 GLN 44 44 ? ? ? A . n A 1 45 GLN 45 45 ? ? ? A . n A 1 46 ALA 46 46 ? ? ? A . n A 1 47 THR 47 47 ? ? ? A . n A 1 48 PRO 48 48 ? ? ? A . n A 1 49 GLY 49 49 ? ? ? A . n A 1 50 GLY 50 50 ? ? ? A . n A 1 51 ALA 51 51 ? ? ? A . n A 1 52 ALA 52 52 ? ? ? A . n A 1 53 PRO 53 53 ? ? ? A . n A 1 54 THR 54 54 ? ? ? A . n A 1 55 ILE 55 55 ? ? ? A . n A 1 56 PHE 56 56 ? ? ? A . n A 1 57 SER 57 57 ? ? ? A . n A 1 58 ARG 58 58 ? ? ? A . n A 1 59 ILE 59 59 ? ? ? A . n A 1 60 LEU 60 60 ? ? ? A . n A 1 61 ASP 61 61 ? ? ? A . n A 1 62 LYS 62 62 ? ? ? A . n A 1 63 SER 63 63 ? ? ? A . n A 1 64 LEU 64 64 ? ? ? A . n A 1 65 PRO 65 65 65 PRO ALA A . n A 1 66 ALA 66 66 66 ALA ALA A . n A 1 67 ASP 67 67 67 ASP ASP A . n A 1 68 ILE 68 68 68 ILE ILE A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 TYR 70 70 70 TYR TYR A . n A 1 71 GLU 71 71 71 GLU GLU A . n A 1 72 ASP 72 72 72 ASP ASP A . n A 1 73 GLN 73 73 73 GLN GLN A . n A 1 74 GLN 74 74 74 GLN GLN A . n A 1 75 CYS 75 75 75 CYS CYS A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 PHE 78 78 78 PHE PHE A . n A 1 79 ARG 79 79 79 ARG ARG A . n A 1 80 ASP 80 80 80 ASP ASP A . n A 1 81 VAL 81 81 81 VAL VAL A . n A 1 82 ALA 82 82 82 ALA ALA A . n A 1 83 PRO 83 83 83 PRO PRO A . n A 1 84 GLN 84 84 84 GLN GLN A . n A 1 85 ALA 85 85 85 ALA ALA A . n A 1 86 PRO 86 86 86 PRO PRO A . n A 1 87 VAL 87 87 87 VAL VAL A . n A 1 88 HIS 88 88 88 HIS HIS A . n A 1 89 PHE 89 89 89 PHE PHE A . n A 1 90 LEU 90 90 90 LEU LEU A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 ILE 92 92 92 ILE ILE A . n A 1 93 PRO 93 93 93 PRO PRO A . n A 1 94 LYS 94 94 94 LYS LYS A . n A 1 95 LYS 95 95 95 LYS LYS A . n A 1 96 PRO 96 96 96 PRO PRO A . n A 1 97 ILE 97 97 97 ILE ILE A . n A 1 98 PRO 98 98 98 PRO PRO A . n A 1 99 ARG 99 99 99 ARG ARG A . n A 1 100 ILE 100 100 100 ILE ILE A . n A 1 101 SER 101 101 101 SER SER A . n A 1 102 GLN 102 102 102 GLN GLN A . n A 1 103 ALA 103 103 103 ALA ALA A . n A 1 104 GLU 104 104 104 GLU GLU A . n A 1 105 GLU 105 105 105 GLU GLU A . n A 1 106 GLU 106 106 106 GLU GLU A . n A 1 107 ASP 107 107 107 ASP ASP A . n A 1 108 GLN 108 108 108 GLN GLN A . n A 1 109 GLN 109 109 109 GLN GLN A . n A 1 110 LEU 110 110 110 LEU LEU A . n A 1 111 LEU 111 111 111 LEU LEU A . n A 1 112 GLY 112 112 112 GLY GLY A . n A 1 113 HIS 113 113 113 HIS HIS A . n A 1 114 LEU 114 114 114 LEU LEU A . n A 1 115 LEU 115 115 115 LEU LEU A . n A 1 116 LEU 116 116 116 LEU LEU A . n A 1 117 VAL 117 117 117 VAL VAL A . n A 1 118 ALA 118 118 118 ALA ALA A . n A 1 119 LYS 119 119 119 LYS LYS A . n A 1 120 GLN 120 120 120 GLN GLN A . n A 1 121 THR 121 121 121 THR THR A . n A 1 122 ALA 122 122 122 ALA ALA A . n A 1 123 LYS 123 123 123 LYS LYS A . n A 1 124 ALA 124 124 124 ALA ALA A . n A 1 125 GLU 125 125 125 GLU GLU A . n A 1 126 GLY 126 126 126 GLY GLY A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 GLY 128 128 128 GLY GLY A . n A 1 129 ASP 129 129 129 ASP ASP A . n A 1 130 GLY 130 130 130 GLY GLY A . n A 1 131 TYR 131 131 131 TYR TYR A . n A 1 132 ARG 132 132 132 ARG ARG A . n A 1 133 LEU 133 133 133 LEU LEU A . n A 1 134 VAL 134 134 134 VAL VAL A . n A 1 135 ILE 135 135 135 ILE ILE A . n A 1 136 ASN 136 136 136 ASN ASN A . n A 1 137 ASP 137 137 137 ASP ASP A . n A 1 138 GLY 138 138 138 GLY GLY A . n A 1 139 LYS 139 139 139 LYS LYS A . n A 1 140 LEU 140 140 140 LEU LEU A . n A 1 141 GLY 141 141 141 GLY GLY A . n A 1 142 ALA 142 142 142 ALA ALA A . n A 1 143 GLN 143 143 143 GLN GLN A . n A 1 144 SER 144 144 144 SER SER A . n A 1 145 VAL 145 145 145 VAL VAL A . n A 1 146 TYR 146 146 146 TYR TYR A . n A 1 147 HIS 147 147 147 HIS HIS A . n A 1 148 LEU 148 148 148 LEU LEU A . n A 1 149 HIS 149 149 149 HIS HIS A . n A 1 150 ILE 150 150 150 ILE ILE A . n A 1 151 HIS 151 151 151 HIS HIS A . n A 1 152 VAL 152 152 152 VAL VAL A . n A 1 153 LEU 153 153 153 LEU LEU A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 GLY 155 155 155 GLY GLY A . n A 1 156 ARG 156 156 156 ARG ARG A . n A 1 157 GLN 157 157 157 GLN GLN A . n A 1 158 LEU 158 158 158 LEU LEU A . n A 1 159 GLN 159 159 159 GLN GLN A . n A 1 160 TRP 160 160 160 TRP TRP A . n A 1 161 PRO 161 161 161 PRO PRO A . n A 1 162 PRO 162 162 162 PRO PRO A . n A 1 163 GLY 163 163 163 GLY GLY A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PO4 1 201 1 PO4 PO4 A . C 3 HOH 1 301 1 HOH HOH A . C 3 HOH 2 302 2 HOH HOH A . C 3 HOH 3 303 3 HOH HOH A . C 3 HOH 4 304 4 HOH HOH A . C 3 HOH 5 305 5 HOH HOH A . C 3 HOH 6 306 6 HOH HOH A . C 3 HOH 7 307 7 HOH HOH A . C 3 HOH 8 308 8 HOH HOH A . C 3 HOH 9 309 9 HOH HOH A . C 3 HOH 10 310 10 HOH HOH A . C 3 HOH 11 311 11 HOH HOH A . C 3 HOH 12 312 12 HOH HOH A . C 3 HOH 13 313 13 HOH HOH A . C 3 HOH 14 314 14 HOH HOH A . C 3 HOH 15 315 15 HOH HOH A . C 3 HOH 16 316 16 HOH HOH A . C 3 HOH 17 317 17 HOH HOH A . C 3 HOH 18 318 18 HOH HOH A . C 3 HOH 19 319 19 HOH HOH A . C 3 HOH 20 320 20 HOH HOH A . C 3 HOH 21 321 21 HOH HOH A . C 3 HOH 22 322 22 HOH HOH A . C 3 HOH 23 323 23 HOH HOH A . C 3 HOH 24 324 24 HOH HOH A . C 3 HOH 25 325 25 HOH HOH A . C 3 HOH 26 326 26 HOH HOH A . C 3 HOH 27 327 27 HOH HOH A . C 3 HOH 28 328 28 HOH HOH A . C 3 HOH 29 329 29 HOH HOH A . C 3 HOH 30 330 30 HOH HOH A . C 3 HOH 31 331 31 HOH HOH A . C 3 HOH 32 332 32 HOH HOH A . C 3 HOH 33 333 33 HOH HOH A . C 3 HOH 34 334 34 HOH HOH A . C 3 HOH 35 335 35 HOH HOH A . C 3 HOH 36 336 36 HOH HOH A . C 3 HOH 37 337 37 HOH HOH A . C 3 HOH 38 338 38 HOH HOH A . C 3 HOH 39 339 39 HOH HOH A . C 3 HOH 40 340 40 HOH HOH A . C 3 HOH 41 341 41 HOH HOH A . C 3 HOH 42 342 42 HOH HOH A . C 3 HOH 43 343 43 HOH HOH A . C 3 HOH 44 344 44 HOH HOH A . C 3 HOH 45 345 45 HOH HOH A . C 3 HOH 46 346 46 HOH HOH A . C 3 HOH 47 347 47 HOH HOH A . C 3 HOH 48 348 48 HOH HOH A . C 3 HOH 49 349 49 HOH HOH A . C 3 HOH 50 350 50 HOH HOH A . C 3 HOH 51 351 51 HOH HOH A . C 3 HOH 52 352 52 HOH HOH A . C 3 HOH 53 353 53 HOH HOH A . C 3 HOH 54 354 54 HOH HOH A . C 3 HOH 55 355 55 HOH HOH A . C 3 HOH 56 356 56 HOH HOH A . C 3 HOH 57 357 57 HOH HOH A . C 3 HOH 58 358 58 HOH HOH A . C 3 HOH 59 359 59 HOH HOH A . C 3 HOH 60 360 60 HOH HOH A . C 3 HOH 61 361 61 HOH HOH A . C 3 HOH 62 362 62 HOH HOH A . C 3 HOH 63 363 63 HOH HOH A . C 3 HOH 64 364 64 HOH HOH A . C 3 HOH 65 365 65 HOH HOH A . C 3 HOH 66 366 66 HOH HOH A . C 3 HOH 67 367 67 HOH HOH A . C 3 HOH 68 368 68 HOH HOH A . C 3 HOH 69 369 69 HOH HOH A . C 3 HOH 70 370 70 HOH HOH A . C 3 HOH 71 371 71 HOH HOH A . C 3 HOH 72 372 72 HOH HOH A . C 3 HOH 73 373 73 HOH HOH A . C 3 HOH 74 374 74 HOH HOH A . C 3 HOH 75 375 75 HOH HOH A . C 3 HOH 76 376 76 HOH HOH A . C 3 HOH 77 377 77 HOH HOH A . C 3 HOH 78 378 78 HOH HOH A . C 3 HOH 79 379 79 HOH HOH A . C 3 HOH 80 380 80 HOH HOH A . C 3 HOH 81 381 81 HOH HOH A . C 3 HOH 82 382 82 HOH HOH A . C 3 HOH 83 383 83 HOH HOH A . C 3 HOH 84 384 84 HOH HOH A . C 3 HOH 85 385 85 HOH HOH A . C 3 HOH 86 386 86 HOH HOH A . C 3 HOH 87 387 87 HOH HOH A . C 3 HOH 88 388 88 HOH HOH A . C 3 HOH 89 389 89 HOH HOH A . C 3 HOH 90 390 90 HOH HOH A . C 3 HOH 91 391 91 HOH HOH A . C 3 HOH 92 392 92 HOH HOH A . C 3 HOH 93 393 93 HOH HOH A . C 3 HOH 94 394 94 HOH HOH A . C 3 HOH 95 395 95 HOH HOH A . C 3 HOH 96 396 96 HOH HOH A . C 3 HOH 97 397 97 HOH HOH A . C 3 HOH 98 398 98 HOH HOH A . C 3 HOH 99 399 99 HOH HOH A . C 3 HOH 100 400 100 HOH HOH A . C 3 HOH 101 401 101 HOH HOH A . C 3 HOH 102 402 102 HOH HOH A . C 3 HOH 103 403 103 HOH HOH A . C 3 HOH 104 404 104 HOH HOH A . C 3 HOH 105 405 105 HOH HOH A . C 3 HOH 106 406 106 HOH HOH A . C 3 HOH 107 407 107 HOH HOH A . C 3 HOH 108 408 108 HOH HOH A . C 3 HOH 109 409 109 HOH HOH A . C 3 HOH 110 410 110 HOH HOH A . C 3 HOH 111 411 111 HOH HOH A . C 3 HOH 112 412 112 HOH HOH A . C 3 HOH 113 413 113 HOH HOH A . C 3 HOH 114 414 114 HOH HOH A . C 3 HOH 115 415 115 HOH HOH A . C 3 HOH 116 416 116 HOH HOH A . C 3 HOH 117 417 117 HOH HOH A . C 3 HOH 118 418 118 HOH HOH A . C 3 HOH 119 419 119 HOH HOH A . C 3 HOH 120 420 120 HOH HOH A . C 3 HOH 121 421 121 HOH HOH A . C 3 HOH 122 422 122 HOH HOH A . C 3 HOH 123 423 123 HOH HOH A . C 3 HOH 124 424 124 HOH HOH A . C 3 HOH 125 425 125 HOH HOH A . C 3 HOH 126 426 126 HOH HOH A . C 3 HOH 127 427 127 HOH HOH A . C 3 HOH 128 428 128 HOH HOH A . C 3 HOH 129 429 129 HOH HOH A . C 3 HOH 130 430 130 HOH HOH A . C 3 HOH 131 431 131 HOH HOH A . C 3 HOH 132 432 132 HOH HOH A . C 3 HOH 133 433 133 HOH HOH A . C 3 HOH 134 434 134 HOH HOH A . C 3 HOH 135 435 135 HOH HOH A . C 3 HOH 136 436 136 HOH HOH A . C 3 HOH 137 437 137 HOH HOH A . C 3 HOH 138 438 138 HOH HOH A . C 3 HOH 139 439 139 HOH HOH A . C 3 HOH 140 440 140 HOH HOH A . C 3 HOH 141 441 141 HOH HOH A . C 3 HOH 142 442 142 HOH HOH A . C 3 HOH 143 443 143 HOH HOH A . C 3 HOH 144 444 144 HOH HOH A . C 3 HOH 145 445 145 HOH HOH A . C 3 HOH 146 446 146 HOH HOH A . C 3 HOH 147 447 147 HOH HOH A . C 3 HOH 148 448 148 HOH HOH A . C 3 HOH 149 449 149 HOH HOH A . C 3 HOH 150 450 150 HOH HOH A . C 3 HOH 151 451 151 HOH HOH A . C 3 HOH 152 452 152 HOH HOH A . C 3 HOH 153 453 153 HOH HOH A . C 3 HOH 154 454 154 HOH HOH A . C 3 HOH 155 455 155 HOH HOH A . C 3 HOH 156 456 156 HOH HOH A . C 3 HOH 157 457 157 HOH HOH A . C 3 HOH 158 458 158 HOH HOH A . C 3 HOH 159 459 159 HOH HOH A . C 3 HOH 160 460 160 HOH HOH A . C 3 HOH 161 461 161 HOH HOH A . C 3 HOH 162 462 162 HOH HOH A . C 3 HOH 163 463 163 HOH HOH A . C 3 HOH 164 464 164 HOH HOH A . C 3 HOH 165 465 165 HOH HOH A . C 3 HOH 166 466 166 HOH HOH A . C 3 HOH 167 467 167 HOH HOH A . C 3 HOH 168 468 168 HOH HOH A . C 3 HOH 169 469 169 HOH HOH A . C 3 HOH 170 470 170 HOH HOH A . C 3 HOH 171 471 171 HOH HOH A . C 3 HOH 172 472 172 HOH HOH A . C 3 HOH 173 473 173 HOH HOH A . C 3 HOH 174 474 174 HOH HOH A . C 3 HOH 175 475 175 HOH HOH A . C 3 HOH 176 476 176 HOH HOH A . C 3 HOH 177 477 177 HOH HOH A . C 3 HOH 178 478 178 HOH HOH A . C 3 HOH 179 479 179 HOH HOH A . C 3 HOH 180 480 180 HOH HOH A . C 3 HOH 181 481 181 HOH HOH A . C 3 HOH 182 482 182 HOH HOH A . C 3 HOH 183 483 183 HOH HOH A . C 3 HOH 184 484 184 HOH HOH A . C 3 HOH 185 485 185 HOH HOH A . C 3 HOH 186 486 186 HOH HOH A . C 3 HOH 187 487 187 HOH HOH A . C 3 HOH 188 488 188 HOH HOH A . C 3 HOH 189 489 189 HOH HOH A . C 3 HOH 190 490 190 HOH HOH A . C 3 HOH 191 491 191 HOH HOH A . C 3 HOH 192 492 192 HOH HOH A . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B,C 2 1,3 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)' 4360 ? 1 MORE -34 ? 1 'SSA (A^2)' 8700 ? 2 'ABSA (A^2)' 1820 ? 2 MORE -30 ? 2 'SSA (A^2)' 11240 ? # 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' 4_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 3 'crystal symmetry operation' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5000000000 -0.8660254038 0.0000000000 35.8665000000 -0.8660254038 0.5000000000 0.0000000000 20.7075334299 0.0000000000 0.0000000000 -1.0000000000 34.1756666667 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 318 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-12-11 2 'Structure model' 1 1 2018-03-07 3 'Structure model' 1 2 2020-04-29 # 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 _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Obsolete ? ? # 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' 'Data collection' 2 3 'Structure model' Advisory 3 3 'Structure model' Other # 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 2 'Structure model' diffrn_source 2 3 'Structure model' pdbx_database_PDB_obs_spr 3 3 'Structure model' pdbx_database_status # 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 2 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 2 3 'Structure model' '_pdbx_database_status.status_code' 3 3 'Structure model' '_pdbx_database_status.status_code_sf' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MxCuBE 'data collection' . ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.8.0049 ? 3 XDS 'data reduction' . ? 4 Aimless 'data scaling' 0.1.30 ? 5 # _pdbx_entry_details.entry_id 4NJY _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;UPON CRYSTALLIZATION AUTHORS OBSERVED A TRUNCATION OF PROTEIN CHAIN, CONFIRMED BY MASS SPECTROSCOPY OF OBTAINED CRYSTALS. THE RESULT SHOW FOUR MAJOR FRACTIONS WITH 102, 106, 118 AND 120 AA, BUT IN SOLVED STRUCTURE WE OBSERVED CHAINS WITH LENGTH 110 AND 100 AA, WHAT IS MORE OR LESS IN AGREEMENT WITH MS RESULTS ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 CE1 A HIS 149 ? A O A HOH 301 ? ? 1.71 2 1 NE2 A GLN 102 ? B O A HOH 401 ? ? 1.83 3 1 NE2 A HIS 149 ? A O4 A PO4 201 ? ? 1.95 4 1 O A HOH 313 ? ? O A HOH 472 ? ? 2.02 5 1 O A HOH 379 ? ? O A HOH 488 ? ? 2.03 6 1 O A HOH 313 ? ? O A HOH 467 ? ? 2.05 7 1 O A HOH 413 ? ? O A HOH 467 ? ? 2.09 8 1 O A HOH 464 ? ? O A HOH 467 ? ? 2.09 9 1 O A HOH 332 ? ? O A HOH 334 ? ? 2.12 10 1 NE2 A GLN 120 ? B O A HOH 476 ? ? 2.13 11 1 O A HOH 337 ? ? O A HOH 472 ? ? 2.14 12 1 OE1 A GLN 102 ? B O A HOH 442 ? ? 2.19 13 1 NE2 A HIS 149 ? A P A PO4 201 ? ? 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N A PRO 65 ? ? CA A PRO 65 ? ? CB A PRO 65 ? ? 111.42 103.30 8.12 1.20 N 2 1 CB A ASP 80 ? ? CG A ASP 80 ? ? OD2 A ASP 80 ? ? 124.20 118.30 5.90 0.90 N 3 1 CB A ILE 92 ? A CA A ILE 92 ? A C A ILE 92 ? A 99.36 111.60 -12.24 2.00 N 4 1 CB A ASP 107 ? ? CG A ASP 107 ? ? OD1 A ASP 107 ? ? 112.78 118.30 -5.52 0.90 N 5 1 CB A ASP 129 ? B CG A ASP 129 ? B OD1 A ASP 129 ? B 124.67 118.30 6.37 0.90 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 ALA A 66 ? ? -137.94 -62.76 2 1 ASP A 67 ? ? -62.27 1.22 3 1 LEU A 127 ? ? -92.68 46.60 # 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 PRO 65 ? CG ? A PRO 65 CG 2 1 Y 1 A PRO 65 ? CD ? A PRO 65 CD # 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 MET 1 ? A MET 1 2 1 Y 1 A ALA 2 ? A ALA 2 3 1 Y 1 A ALA 3 ? A ALA 3 4 1 Y 1 A ALA 4 ? A ALA 4 5 1 Y 1 A VAL 5 ? A VAL 5 6 1 Y 1 A VAL 6 ? A VAL 6 7 1 Y 1 A LEU 7 ? A LEU 7 8 1 Y 1 A ALA 8 ? A ALA 8 9 1 Y 1 A ALA 9 ? A ALA 9 10 1 Y 1 A GLY 10 ? A GLY 10 11 1 Y 1 A LEU 11 ? A LEU 11 12 1 Y 1 A ARG 12 ? A ARG 12 13 1 Y 1 A ALA 13 ? A ALA 13 14 1 Y 1 A ALA 14 ? A ALA 14 15 1 Y 1 A ARG 15 ? A ARG 15 16 1 Y 1 A ARG 16 ? A ARG 16 17 1 Y 1 A ALA 17 ? A ALA 17 18 1 Y 1 A VAL 18 ? A VAL 18 19 1 Y 1 A ALA 19 ? A ALA 19 20 1 Y 1 A ALA 20 ? A ALA 20 21 1 Y 1 A THR 21 ? A THR 21 22 1 Y 1 A GLY 22 ? A GLY 22 23 1 Y 1 A VAL 23 ? A VAL 23 24 1 Y 1 A ARG 24 ? A ARG 24 25 1 Y 1 A GLY 25 ? A GLY 25 26 1 Y 1 A GLY 26 ? A GLY 26 27 1 Y 1 A GLN 27 ? A GLN 27 28 1 Y 1 A VAL 28 ? A VAL 28 29 1 Y 1 A ARG 29 ? A ARG 29 30 1 Y 1 A GLY 30 ? A GLY 30 31 1 Y 1 A ALA 31 ? A ALA 31 32 1 Y 1 A ALA 32 ? A ALA 32 33 1 Y 1 A GLY 33 ? A GLY 33 34 1 Y 1 A VAL 34 ? A VAL 34 35 1 Y 1 A THR 35 ? A THR 35 36 1 Y 1 A ASP 36 ? A ASP 36 37 1 Y 1 A GLY 37 ? A GLY 37 38 1 Y 1 A ASN 38 ? A ASN 38 39 1 Y 1 A GLU 39 ? A GLU 39 40 1 Y 1 A VAL 40 ? A VAL 40 41 1 Y 1 A ALA 41 ? A ALA 41 42 1 Y 1 A LYS 42 ? A LYS 42 43 1 Y 1 A ALA 43 ? A ALA 43 44 1 Y 1 A GLN 44 ? A GLN 44 45 1 Y 1 A GLN 45 ? A GLN 45 46 1 Y 1 A ALA 46 ? A ALA 46 47 1 Y 1 A THR 47 ? A THR 47 48 1 Y 1 A PRO 48 ? A PRO 48 49 1 Y 1 A GLY 49 ? A GLY 49 50 1 Y 1 A GLY 50 ? A GLY 50 51 1 Y 1 A ALA 51 ? A ALA 51 52 1 Y 1 A ALA 52 ? A ALA 52 53 1 Y 1 A PRO 53 ? A PRO 53 54 1 Y 1 A THR 54 ? A THR 54 55 1 Y 1 A ILE 55 ? A ILE 55 56 1 Y 1 A PHE 56 ? A PHE 56 57 1 Y 1 A SER 57 ? A SER 57 58 1 Y 1 A ARG 58 ? A ARG 58 59 1 Y 1 A ILE 59 ? A ILE 59 60 1 Y 1 A LEU 60 ? A LEU 60 61 1 Y 1 A ASP 61 ? A ASP 61 62 1 Y 1 A LYS 62 ? A LYS 62 63 1 Y 1 A SER 63 ? A SER 63 64 1 Y 1 A LEU 64 ? A LEU 64 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PHOSPHATE ION' PO4 3 water HOH #