data_3NOH # _entry.id 3NOH # _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 3NOH pdb_00003noh 10.2210/pdb3noh/pdb RCSB RCSB060082 ? ? WWPDB D_1000060082 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 417426 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3NOH _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-25 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a putative peptide binding protein (RUMGNA_00914) from Ruminococcus gnavus ATCC 29149 at 1.60 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 3NOH _cell.length_a 62.963 _cell.length_b 62.963 _cell.length_c 52.978 _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 3NOH _symmetry.Int_Tables_number 152 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'putative peptide binding protein' 15468.719 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 water nat water 18.015 109 ? ? ? ? # _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 ;GVTGATPKAKKAAQSSAQLEGSYIFC(MSE)NPLLDKLSDEDIREQLKAFVTGKTDSIRTDTELSFDIYVSETDYALIRY ADSLCERLNDAGADVQIKQYSGT(MSE)LRSRAVSGKYEAFLSESDLVSTDALENADYIILDSAE(MSE)R ; _entity_poly.pdbx_seq_one_letter_code_can ;GVTGATPKAKKAAQSSAQLEGSYIFCMNPLLDKLSDEDIREQLKAFVTGKTDSIRTDTELSFDIYVSETDYALIRYADSL CERLNDAGADVQIKQYSGTMLRSRAVSGKYEAFLSESDLVSTDALENADYIILDSAEMR ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 417426 # 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 VAL n 1 3 THR n 1 4 GLY n 1 5 ALA n 1 6 THR n 1 7 PRO n 1 8 LYS n 1 9 ALA n 1 10 LYS n 1 11 LYS n 1 12 ALA n 1 13 ALA n 1 14 GLN n 1 15 SER n 1 16 SER n 1 17 ALA n 1 18 GLN n 1 19 LEU n 1 20 GLU n 1 21 GLY n 1 22 SER n 1 23 TYR n 1 24 ILE n 1 25 PHE n 1 26 CYS n 1 27 MSE n 1 28 ASN n 1 29 PRO n 1 30 LEU n 1 31 LEU n 1 32 ASP n 1 33 LYS n 1 34 LEU n 1 35 SER n 1 36 ASP n 1 37 GLU n 1 38 ASP n 1 39 ILE n 1 40 ARG n 1 41 GLU n 1 42 GLN n 1 43 LEU n 1 44 LYS n 1 45 ALA n 1 46 PHE n 1 47 VAL n 1 48 THR n 1 49 GLY n 1 50 LYS n 1 51 THR n 1 52 ASP n 1 53 SER n 1 54 ILE n 1 55 ARG n 1 56 THR n 1 57 ASP n 1 58 THR n 1 59 GLU n 1 60 LEU n 1 61 SER n 1 62 PHE n 1 63 ASP n 1 64 ILE n 1 65 TYR n 1 66 VAL n 1 67 SER n 1 68 GLU n 1 69 THR n 1 70 ASP n 1 71 TYR n 1 72 ALA n 1 73 LEU n 1 74 ILE n 1 75 ARG n 1 76 TYR n 1 77 ALA n 1 78 ASP n 1 79 SER n 1 80 LEU n 1 81 CYS n 1 82 GLU n 1 83 ARG n 1 84 LEU n 1 85 ASN n 1 86 ASP n 1 87 ALA n 1 88 GLY n 1 89 ALA n 1 90 ASP n 1 91 VAL n 1 92 GLN n 1 93 ILE n 1 94 LYS n 1 95 GLN n 1 96 TYR n 1 97 SER n 1 98 GLY n 1 99 THR n 1 100 MSE n 1 101 LEU n 1 102 ARG n 1 103 SER n 1 104 ARG n 1 105 ALA n 1 106 VAL n 1 107 SER n 1 108 GLY n 1 109 LYS n 1 110 TYR n 1 111 GLU n 1 112 ALA n 1 113 PHE n 1 114 LEU n 1 115 SER n 1 116 GLU n 1 117 SER n 1 118 ASP n 1 119 LEU n 1 120 VAL n 1 121 SER n 1 122 THR n 1 123 ASP n 1 124 ALA n 1 125 LEU n 1 126 GLU n 1 127 ASN n 1 128 ALA n 1 129 ASP n 1 130 TYR n 1 131 ILE n 1 132 ILE n 1 133 LEU n 1 134 ASP n 1 135 SER n 1 136 ALA n 1 137 GLU n 1 138 MSE n 1 139 ARG 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 TBD _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene RUMGNA_00914 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 29149' _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 'Ruminococcus gnavus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 411470 _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 A7B039_RUMGN _struct_ref.pdbx_db_accession A7B039 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VTGATPKAKKAAQSSAQLEGSYIFCMNPLLDKLSDEDIREQLKAFVTGKTDSIRTDTELSFDIYVSETDYALIRYADSLC ERLNDAGADVQIKQYSGTMLRSRAVSGKYEAFLSESDLVSTDALENADYIILDSAEMR ; _struct_ref.pdbx_align_begin 32 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NOH _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 139 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A7B039 _struct_ref_seq.db_align_beg 32 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 169 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 32 _struct_ref_seq.pdbx_auth_seq_align_end 169 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3NOH _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 A7B039 _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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 3NOH # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.96 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 37.24 _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 5.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '2.400000000M (NH4)2SO4, 0.1M Citrate pH 5.0, 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 mirror (vertical focusing)' _diffrn_detector.pdbx_collection_date 2010-06-10 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91837 1.0 2 0.97917 1.0 3 0.97874 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.91837,0.97917,0.97874 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3NOH _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 27.264 _reflns.number_obs 16202 _reflns.pdbx_Rmerge_I_obs 0.034 _reflns.pdbx_netI_over_sigmaI 20.910 _reflns.percent_possible_obs 98.800 _reflns.B_iso_Wilson_estimate 23.830 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 1.600 1.660 12098 ? 3193 0.628 2.5 ? ? ? ? ? 97.300 ? 1 1.660 1.720 10492 ? 2739 0.478 3.3 ? ? ? ? ? 98.600 ? 2 1.720 1.800 12050 ? 3148 0.312 4.8 ? ? ? ? ? 98.700 ? 3 1.800 1.900 12374 ? 3229 0.207 6.9 ? ? ? ? ? 98.500 ? 4 1.900 2.020 11752 ? 3069 0.115 11.5 ? ? ? ? ? 98.900 ? 5 2.020 2.170 11430 ? 2966 0.074 16.8 ? ? ? ? ? 99.300 ? 6 2.170 2.390 11852 ? 3089 0.049 23.7 ? ? ? ? ? 99.300 ? 7 2.390 2.730 11838 ? 3067 0.035 32.3 ? ? ? ? ? 99.600 ? 8 2.730 3.440 11968 ? 3109 0.023 45.9 ? ? ? ? ? 99.700 ? 9 3.440 27.264 11783 ? 3089 0.018 60.6 ? ? ? ? ? 98.600 ? 10 # _refine.entry_id 3NOH _refine.ls_d_res_high 1.6000 _refine.ls_d_res_low 27.264 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 98.8200 _refine.ls_number_reflns_obs 16192 _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.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.SULFATE (SO4) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1612 _refine.ls_R_factor_R_work 0.1596 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1956 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_number_reflns_R_free 821 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 33.7307 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.4800 _refine.aniso_B[2][2] 1.4800 _refine.aniso_B[3][3] -2.2200 _refine.aniso_B[1][2] 0.7400 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9740 _refine.correlation_coeff_Fo_to_Fc_free 0.9590 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.0880 _refine.overall_SU_ML 0.0640 _refine.overall_SU_B 3.6290 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 88.890 _refine.B_iso_min 15.210 _refine.occupancy_max 1.000 _refine.occupancy_min 0.150 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 953 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 109 _refine_hist.number_atoms_total 1073 _refine_hist.d_res_high 1.6000 _refine_hist.d_res_low 27.264 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1077 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 729 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1479 1.598 1.995 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1805 1.016 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 152 5.365 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 51 36.887 24.706 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 205 12.691 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 8 15.391 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 174 0.111 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1226 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 218 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 661 1.896 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 266 0.596 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1083 3.028 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 416 4.789 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 379 6.993 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.6000 _refine_ls_shell.d_res_low 1.6420 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 97.6400 _refine_ls_shell.number_reflns_R_work 1086 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2590 _refine_ls_shell.R_factor_R_free 0.3180 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 72 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1158 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3NOH _struct.title 'Crystal structure of a putative peptide binding protein (RUMGNA_00914) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y _struct.pdbx_model_type_details ? # _struct_keywords.text 'Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, PEPTIDE BINDING PROTEIN' _struct_keywords.pdbx_keywords 'PEPTIDE BINDING PROTEIN' _struct_keywords.entry_id 3NOH # 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 ? D N N 4 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS 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 LEU A 31 ? SER A 35 ? LEU A 61 SER A 65 5 ? 5 HELX_P HELX_P2 2 ASP A 36 ? THR A 48 ? ASP A 66 THR A 78 1 ? 13 HELX_P HELX_P3 3 ASP A 70 ? ALA A 87 ? ASP A 100 ALA A 117 1 ? 18 HELX_P HELX_P4 4 SER A 97 ? GLY A 108 ? SER A 127 GLY A 138 1 ? 12 HELX_P HELX_P5 5 SER A 121 ? ASN A 127 ? SER A 151 ASN A 157 1 ? 7 HELX_P HELX_P6 6 ALA A 136 ? MSE A 138 ? ALA A 166 MSE A 168 5 ? 3 # _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 CYS 26 C ? ? ? 1_555 A MSE 27 N ? ? A CYS 56 A MSE 57 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale2 covale both ? A MSE 27 C ? ? ? 1_555 A ASN 28 N ? ? A MSE 57 A ASN 58 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale3 covale both ? A THR 99 C ? ? ? 1_555 A MSE 100 N ? ? A THR 129 A MSE 130 1_555 ? ? ? ? ? ? ? 1.345 ? ? covale4 covale both ? A MSE 100 C ? ? ? 1_555 A LEU 101 N ? ? A MSE 130 A LEU 131 1_555 ? ? ? ? ? ? ? 1.341 ? ? covale5 covale both ? A GLU 137 C ? ? ? 1_555 A MSE 138 N ? ? A GLU 167 A MSE 168 1_555 ? ? ? ? ? ? ? 1.340 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _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 ? parallel A 2 3 ? 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 ASP A 90 ? TYR A 96 ? ASP A 120 TYR A 126 A 2 SER A 61 ? SER A 67 ? SER A 91 SER A 97 A 3 ALA A 112 ? GLU A 116 ? ALA A 142 GLU A 146 A 4 SER A 22 ? MSE A 27 ? SER A 52 MSE A 57 A 5 ASP A 129 ? ASP A 134 ? ASP A 159 ASP A 164 # 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 GLN A 92 ? O GLN A 122 N ILE A 64 ? N ILE A 94 A 2 3 N TYR A 65 ? N TYR A 95 O ALA A 112 ? O ALA A 142 A 3 4 O SER A 115 ? O SER A 145 N ILE A 24 ? N ILE A 54 A 4 5 N TYR A 23 ? N TYR A 53 O LEU A 133 ? O LEU A 163 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GOL 200 ? 9 'BINDING SITE FOR RESIDUE GOL A 200' AC2 Software A SO4 201 ? 3 'BINDING SITE FOR RESIDUE SO4 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 9 TYR A 96 ? TYR A 126 . ? 2_665 ? 2 AC1 9 ARG A 102 ? ARG A 132 . ? 1_555 ? 3 AC1 9 ARG A 104 ? ARG A 134 . ? 2_665 ? 4 AC1 9 SER A 121 ? SER A 151 . ? 1_555 ? 5 AC1 9 THR A 122 ? THR A 152 . ? 1_555 ? 6 AC1 9 GLU A 137 ? GLU A 167 . ? 5_675 ? 7 AC1 9 HOH D . ? HOH A 244 . ? 1_555 ? 8 AC1 9 HOH D . ? HOH A 247 . ? 1_555 ? 9 AC1 9 HOH D . ? HOH A 305 . ? 1_555 ? 10 AC2 3 GLN A 18 ? GLN A 48 . ? 1_555 ? 11 AC2 3 ARG A 75 ? ARG A 105 . ? 1_555 ? 12 AC2 3 HOH D . ? HOH A 225 . ? 1_555 ? # _atom_sites.entry_id 3NOH _atom_sites.fract_transf_matrix[1][1] 0.015882 _atom_sites.fract_transf_matrix[1][2] 0.009170 _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] 0.018339 _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] 0.018876 _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 VAL 2 32 ? ? ? A . n A 1 3 THR 3 33 ? ? ? A . n A 1 4 GLY 4 34 ? ? ? A . n A 1 5 ALA 5 35 ? ? ? A . n A 1 6 THR 6 36 ? ? ? A . n A 1 7 PRO 7 37 ? ? ? A . n A 1 8 LYS 8 38 ? ? ? A . n A 1 9 ALA 9 39 ? ? ? A . n A 1 10 LYS 10 40 ? ? ? A . n A 1 11 LYS 11 41 ? ? ? A . n A 1 12 ALA 12 42 ? ? ? A . n A 1 13 ALA 13 43 ? ? ? A . n A 1 14 GLN 14 44 ? ? ? A . n A 1 15 SER 15 45 ? ? ? A . n A 1 16 SER 16 46 46 SER SER A . n A 1 17 ALA 17 47 47 ALA ALA A . n A 1 18 GLN 18 48 48 GLN GLN A . n A 1 19 LEU 19 49 49 LEU LEU A . n A 1 20 GLU 20 50 50 GLU GLU A . n A 1 21 GLY 21 51 51 GLY GLY A . n A 1 22 SER 22 52 52 SER SER A . n A 1 23 TYR 23 53 53 TYR TYR A . n A 1 24 ILE 24 54 54 ILE ILE A . n A 1 25 PHE 25 55 55 PHE PHE A . n A 1 26 CYS 26 56 56 CYS CYS A . n A 1 27 MSE 27 57 57 MSE MSE A . n A 1 28 ASN 28 58 58 ASN ASN A . n A 1 29 PRO 29 59 59 PRO PRO A . n A 1 30 LEU 30 60 60 LEU LEU A . n A 1 31 LEU 31 61 61 LEU LEU A . n A 1 32 ASP 32 62 62 ASP ASP A . n A 1 33 LYS 33 63 63 LYS LYS A . n A 1 34 LEU 34 64 64 LEU LEU A . n A 1 35 SER 35 65 65 SER SER A . n A 1 36 ASP 36 66 66 ASP ASP A . n A 1 37 GLU 37 67 67 GLU GLU A . n A 1 38 ASP 38 68 68 ASP ASP A . n A 1 39 ILE 39 69 69 ILE ILE A . n A 1 40 ARG 40 70 70 ARG ARG A . n A 1 41 GLU 41 71 71 GLU GLU A . n A 1 42 GLN 42 72 72 GLN GLN A . n A 1 43 LEU 43 73 73 LEU LEU A . n A 1 44 LYS 44 74 74 LYS LYS A . n A 1 45 ALA 45 75 75 ALA ALA A . n A 1 46 PHE 46 76 76 PHE PHE A . n A 1 47 VAL 47 77 77 VAL VAL A . n A 1 48 THR 48 78 78 THR THR A . n A 1 49 GLY 49 79 79 GLY GLY A . n A 1 50 LYS 50 80 80 LYS LYS A . n A 1 51 THR 51 81 81 THR THR A . n A 1 52 ASP 52 82 82 ASP ASP A . n A 1 53 SER 53 83 83 SER SER A . n A 1 54 ILE 54 84 84 ILE ILE A . n A 1 55 ARG 55 85 85 ARG ARG A . n A 1 56 THR 56 86 86 THR THR A . n A 1 57 ASP 57 87 87 ASP ASP A . n A 1 58 THR 58 88 88 THR THR A . n A 1 59 GLU 59 89 89 GLU GLU A . n A 1 60 LEU 60 90 90 LEU LEU A . n A 1 61 SER 61 91 91 SER SER A . n A 1 62 PHE 62 92 92 PHE PHE A . n A 1 63 ASP 63 93 93 ASP ASP A . n A 1 64 ILE 64 94 94 ILE ILE A . n A 1 65 TYR 65 95 95 TYR TYR A . n A 1 66 VAL 66 96 96 VAL VAL A . n A 1 67 SER 67 97 97 SER SER A . n A 1 68 GLU 68 98 98 GLU GLU A . n A 1 69 THR 69 99 99 THR THR A . n A 1 70 ASP 70 100 100 ASP ASP A . n A 1 71 TYR 71 101 101 TYR TYR A . n A 1 72 ALA 72 102 102 ALA ALA A . n A 1 73 LEU 73 103 103 LEU LEU A . n A 1 74 ILE 74 104 104 ILE ILE A . n A 1 75 ARG 75 105 105 ARG ARG A . n A 1 76 TYR 76 106 106 TYR TYR A . n A 1 77 ALA 77 107 107 ALA ALA A . n A 1 78 ASP 78 108 108 ASP ASP A . n A 1 79 SER 79 109 109 SER SER A . n A 1 80 LEU 80 110 110 LEU LEU A . n A 1 81 CYS 81 111 111 CYS CYS A . n A 1 82 GLU 82 112 112 GLU GLU A . n A 1 83 ARG 83 113 113 ARG ARG A . n A 1 84 LEU 84 114 114 LEU LEU A . n A 1 85 ASN 85 115 115 ASN ASN A . n A 1 86 ASP 86 116 116 ASP ASP A . n A 1 87 ALA 87 117 117 ALA ALA A . n A 1 88 GLY 88 118 118 GLY GLY A . n A 1 89 ALA 89 119 119 ALA ALA A . n A 1 90 ASP 90 120 120 ASP ASP A . n A 1 91 VAL 91 121 121 VAL VAL A . n A 1 92 GLN 92 122 122 GLN GLN A . n A 1 93 ILE 93 123 123 ILE ILE A . n A 1 94 LYS 94 124 124 LYS LYS A . n A 1 95 GLN 95 125 125 GLN GLN A . n A 1 96 TYR 96 126 126 TYR TYR A . n A 1 97 SER 97 127 127 SER SER A . n A 1 98 GLY 98 128 128 GLY GLY A . n A 1 99 THR 99 129 129 THR THR A . n A 1 100 MSE 100 130 130 MSE MSE A . n A 1 101 LEU 101 131 131 LEU LEU A . n A 1 102 ARG 102 132 132 ARG ARG A . n A 1 103 SER 103 133 133 SER SER A . n A 1 104 ARG 104 134 134 ARG ARG A . n A 1 105 ALA 105 135 135 ALA ALA A . n A 1 106 VAL 106 136 136 VAL VAL A . n A 1 107 SER 107 137 137 SER SER A . n A 1 108 GLY 108 138 138 GLY GLY A . n A 1 109 LYS 109 139 139 LYS LYS A . n A 1 110 TYR 110 140 140 TYR TYR A . n A 1 111 GLU 111 141 141 GLU GLU A . n A 1 112 ALA 112 142 142 ALA ALA A . n A 1 113 PHE 113 143 143 PHE PHE A . n A 1 114 LEU 114 144 144 LEU LEU A . n A 1 115 SER 115 145 145 SER SER A . n A 1 116 GLU 116 146 146 GLU GLU A . n A 1 117 SER 117 147 147 SER SER A . n A 1 118 ASP 118 148 148 ASP ASP A . n A 1 119 LEU 119 149 149 LEU LEU A . n A 1 120 VAL 120 150 150 VAL VAL A . n A 1 121 SER 121 151 151 SER SER A . n A 1 122 THR 122 152 152 THR THR A . n A 1 123 ASP 123 153 153 ASP ASP A . n A 1 124 ALA 124 154 154 ALA ALA A . n A 1 125 LEU 125 155 155 LEU LEU A . n A 1 126 GLU 126 156 156 GLU GLU A . n A 1 127 ASN 127 157 157 ASN ASN A . n A 1 128 ALA 128 158 158 ALA ALA A . n A 1 129 ASP 129 159 159 ASP ASP A . n A 1 130 TYR 130 160 160 TYR TYR A . n A 1 131 ILE 131 161 161 ILE ILE A . n A 1 132 ILE 132 162 162 ILE ILE A . n A 1 133 LEU 133 163 163 LEU LEU A . n A 1 134 ASP 134 164 164 ASP ASP A . n A 1 135 SER 135 165 165 SER SER A . n A 1 136 ALA 136 166 166 ALA ALA A . n A 1 137 GLU 137 167 167 GLU GLU A . n A 1 138 MSE 138 168 168 MSE MSE A . n A 1 139 ARG 139 169 ? ? ? A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 GOL 1 200 200 GOL GOL A . C 3 SO4 1 201 201 SO4 SO4 A . D 4 HOH 1 202 202 HOH HOH A . D 4 HOH 2 203 203 HOH HOH A . D 4 HOH 3 204 204 HOH HOH A . D 4 HOH 4 205 205 HOH HOH A . D 4 HOH 5 206 206 HOH HOH A . D 4 HOH 6 207 207 HOH HOH A . D 4 HOH 7 208 208 HOH HOH A . D 4 HOH 8 209 209 HOH HOH A . D 4 HOH 9 210 210 HOH HOH A . D 4 HOH 10 211 211 HOH HOH A . D 4 HOH 11 212 212 HOH HOH A . D 4 HOH 12 213 213 HOH HOH A . D 4 HOH 13 214 214 HOH HOH A . D 4 HOH 14 215 215 HOH HOH A . D 4 HOH 15 216 216 HOH HOH A . D 4 HOH 16 217 217 HOH HOH A . D 4 HOH 17 218 218 HOH HOH A . D 4 HOH 18 219 219 HOH HOH A . D 4 HOH 19 220 220 HOH HOH A . D 4 HOH 20 221 221 HOH HOH A . D 4 HOH 21 222 222 HOH HOH A . D 4 HOH 22 223 223 HOH HOH A . D 4 HOH 23 224 224 HOH HOH A . D 4 HOH 24 225 225 HOH HOH A . D 4 HOH 25 226 226 HOH HOH A . D 4 HOH 26 227 227 HOH HOH A . D 4 HOH 27 228 228 HOH HOH A . D 4 HOH 28 229 229 HOH HOH A . D 4 HOH 29 230 230 HOH HOH A . D 4 HOH 30 231 231 HOH HOH A . D 4 HOH 31 232 232 HOH HOH A . D 4 HOH 32 233 233 HOH HOH A . D 4 HOH 33 234 234 HOH HOH A . D 4 HOH 34 235 235 HOH HOH A . D 4 HOH 35 236 236 HOH HOH A . D 4 HOH 36 237 237 HOH HOH A . D 4 HOH 37 238 238 HOH HOH A . D 4 HOH 38 239 239 HOH HOH A . D 4 HOH 39 240 240 HOH HOH A . D 4 HOH 40 241 241 HOH HOH A . D 4 HOH 41 242 242 HOH HOH A . D 4 HOH 42 243 243 HOH HOH A . D 4 HOH 43 244 244 HOH HOH A . D 4 HOH 44 245 245 HOH HOH A . D 4 HOH 45 246 246 HOH HOH A . D 4 HOH 46 247 247 HOH HOH A . D 4 HOH 47 248 248 HOH HOH A . D 4 HOH 48 249 249 HOH HOH A . D 4 HOH 49 250 250 HOH HOH A . D 4 HOH 50 251 251 HOH HOH A . D 4 HOH 51 252 252 HOH HOH A . D 4 HOH 52 253 253 HOH HOH A . D 4 HOH 53 254 254 HOH HOH A . D 4 HOH 54 255 255 HOH HOH A . D 4 HOH 55 256 256 HOH HOH A . D 4 HOH 56 257 257 HOH HOH A . D 4 HOH 57 258 258 HOH HOH A . D 4 HOH 58 259 259 HOH HOH A . D 4 HOH 59 260 260 HOH HOH A . D 4 HOH 60 261 261 HOH HOH A . D 4 HOH 61 262 262 HOH HOH A . D 4 HOH 62 263 263 HOH HOH A . D 4 HOH 63 264 264 HOH HOH A . D 4 HOH 64 265 265 HOH HOH A . D 4 HOH 65 266 266 HOH HOH A . D 4 HOH 66 267 267 HOH HOH A . D 4 HOH 67 268 268 HOH HOH A . D 4 HOH 68 269 269 HOH HOH A . D 4 HOH 69 270 270 HOH HOH A . D 4 HOH 70 271 271 HOH HOH A . D 4 HOH 71 272 272 HOH HOH A . D 4 HOH 72 273 273 HOH HOH A . D 4 HOH 73 274 274 HOH HOH A . D 4 HOH 74 275 275 HOH HOH A . D 4 HOH 75 276 276 HOH HOH A . D 4 HOH 76 277 277 HOH HOH A . D 4 HOH 77 278 278 HOH HOH A . D 4 HOH 78 279 279 HOH HOH A . D 4 HOH 79 280 280 HOH HOH A . D 4 HOH 80 281 281 HOH HOH A . D 4 HOH 81 282 282 HOH HOH A . D 4 HOH 82 283 283 HOH HOH A . D 4 HOH 83 284 284 HOH HOH A . D 4 HOH 84 285 285 HOH HOH A . D 4 HOH 85 286 286 HOH HOH A . D 4 HOH 86 287 287 HOH HOH A . D 4 HOH 87 288 288 HOH HOH A . D 4 HOH 88 289 289 HOH HOH A . D 4 HOH 89 290 290 HOH HOH A . D 4 HOH 90 291 291 HOH HOH A . D 4 HOH 91 292 292 HOH HOH A . D 4 HOH 92 293 293 HOH HOH A . D 4 HOH 93 294 294 HOH HOH A . D 4 HOH 94 295 295 HOH HOH A . D 4 HOH 95 296 296 HOH HOH A . D 4 HOH 96 297 297 HOH HOH A . D 4 HOH 97 298 298 HOH HOH A . D 4 HOH 98 299 299 HOH HOH A . D 4 HOH 99 300 300 HOH HOH A . D 4 HOH 100 301 301 HOH HOH A . D 4 HOH 101 302 302 HOH HOH A . D 4 HOH 102 303 303 HOH HOH A . D 4 HOH 103 304 304 HOH HOH A . D 4 HOH 104 305 305 HOH HOH A . D 4 HOH 105 306 306 HOH HOH A . D 4 HOH 106 307 307 HOH HOH A . D 4 HOH 107 308 308 HOH HOH A . D 4 HOH 108 309 309 HOH HOH A . D 4 HOH 109 310 310 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 27 A MSE 57 ? MET SELENOMETHIONINE 2 A MSE 100 A MSE 130 ? MET SELENOMETHIONINE 3 A MSE 138 A MSE 168 ? 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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2010-08-25 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 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' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 3 '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' database_2 2 3 'Structure model' struct_conn 3 3 'Structure model' struct_ref_seq_dif 4 3 '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' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq_dif.details' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 '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 8.4960 _pdbx_refine_tls.origin_y 45.7996 _pdbx_refine_tls.origin_z 8.2322 _pdbx_refine_tls.T[1][1] 0.1092 _pdbx_refine_tls.T[2][2] 0.0062 _pdbx_refine_tls.T[3][3] 0.0742 _pdbx_refine_tls.T[1][2] -0.0145 _pdbx_refine_tls.T[1][3] 0.0135 _pdbx_refine_tls.T[2][3] -0.0117 _pdbx_refine_tls.L[1][1] 2.6287 _pdbx_refine_tls.L[2][2] 2.5558 _pdbx_refine_tls.L[3][3] 3.6481 _pdbx_refine_tls.L[1][2] 0.4654 _pdbx_refine_tls.L[1][3] -0.8171 _pdbx_refine_tls.L[2][3] 0.5697 _pdbx_refine_tls.S[1][1] 0.0020 _pdbx_refine_tls.S[2][2] 0.0988 _pdbx_refine_tls.S[3][3] -0.1008 _pdbx_refine_tls.S[1][2] 0.0135 _pdbx_refine_tls.S[1][3] 0.1971 _pdbx_refine_tls.S[2][3] -0.2207 _pdbx_refine_tls.S[2][1] -0.2087 _pdbx_refine_tls.S[3][1] -0.4823 _pdbx_refine_tls.S[3][2] 0.0978 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _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.beg_auth_seq_id 46 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 168 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # _phasing.method MAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 2 REFMAC 5.5.0110 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 3 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? 6 SHELXD . ? ? ? ? phasing ? ? ? 7 autoSHARP . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 3NOH _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT (RESIDUES 32-169) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. LIQUID CHROMATOGRAPHY MASS SPECTROSCOPY (LC/MS) ANALYSIS OF THE PROTEIN PREP PRIOR TO CRYSTALLIZATION SHOWED THAT APPROXIMATELY 1/3 OF THE SAMPLE WAS MISSING AN ADDITIONAL 10 N-TERMINAL AMINO ACID RESIDUES (G-VTGATPKAK) BEYOND THE ENGINEERED TEV CLEAVAGE SITE AND CORRESPONDS TO RESIDUES 41-169 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id GLU _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 141 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -106.69 _pdbx_validate_torsion.psi -61.70 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 80 ? CE ? A LYS 50 CE 2 1 Y 1 A LYS 80 ? NZ ? A LYS 50 NZ 3 1 Y 1 A ARG 85 ? CD ? A ARG 55 CD 4 1 Y 1 A ARG 85 ? NE ? A ARG 55 NE 5 1 Y 1 A ARG 85 ? CZ ? A ARG 55 CZ 6 1 Y 1 A ARG 85 ? NH1 ? A ARG 55 NH1 7 1 Y 1 A ARG 85 ? NH2 ? A ARG 55 NH2 8 1 Y 1 A GLU 89 ? CD ? A GLU 59 CD 9 1 Y 1 A GLU 89 ? OE1 ? A GLU 59 OE1 10 1 Y 1 A GLU 89 ? OE2 ? A GLU 59 OE2 # 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 VAL 32 ? A VAL 2 3 1 Y 1 A THR 33 ? A THR 3 4 1 Y 1 A GLY 34 ? A GLY 4 5 1 Y 1 A ALA 35 ? A ALA 5 6 1 Y 1 A THR 36 ? A THR 6 7 1 Y 1 A PRO 37 ? A PRO 7 8 1 Y 1 A LYS 38 ? A LYS 8 9 1 Y 1 A ALA 39 ? A ALA 9 10 1 Y 1 A LYS 40 ? A LYS 10 11 1 Y 1 A LYS 41 ? A LYS 11 12 1 Y 1 A ALA 42 ? A ALA 12 13 1 Y 1 A ALA 43 ? A ALA 13 14 1 Y 1 A GLN 44 ? A GLN 14 15 1 Y 1 A SER 45 ? A SER 15 16 1 Y 1 A ARG 169 ? A ARG 139 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 'SULFATE ION' SO4 4 water HOH #