data_3DB3 # _entry.id 3DB3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3DB3 RCSB RCSB047816 WWPDB D_1000047816 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3BI7 ;CRYSTAL STRUCTURE OF THE SRA DOMAIN OF E3 UBIQUITIN-PROTEIN LIGASE UHRF1 ; unspecified PDB 3CLZ ;THE SET AND RING ASSOCIATED (SRA) DOMAIN OF UHRF1 BOUND TO METHYLATED DNA ; unspecified PDB 2FAZ ;UBIQUITIN-LIKE DOMAIN OF HUMAN NUCLEAR ZINC FINGER PROTEIN NP95 ; unspecified PDB 3DB4 'STRUCTURE OF THE TANDEM TUDOR DOMAINS OF THE E3 UBIQUITIN-PROTEIN LIGASE UHRF1' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3DB3 _pdbx_database_status.recvd_initial_deposition_date 2008-05-30 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Walker, J.R.' 1 'Avvakumov, G.V.' 2 'Xue, S.' 3 'Dong, A.' 4 'Li, Y.' 5 'Bountra, C.' 6 'Weigelt, J.' 7 'Arrowsmith, C.H.' 8 'Edwards, A.M.' 9 'Bochkarev, A.' 10 'Dhe-Paganon, S.' 11 'Structural Genomics Consortium (SGC)' 12 # _citation.id primary _citation.title 'Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 286 _citation.page_first 24300 _citation.page_last 24311 _citation.year 2011 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21489993 _citation.pdbx_database_id_DOI 10.1074/jbc.M111.234104 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Nady, N.' 1 primary 'Lemak, A.' 2 primary 'Walker, J.R.' 3 primary 'Avvakumov, G.V.' 4 primary 'Kareta, M.S.' 5 primary 'Achour, M.' 6 primary 'Xue, S.' 7 primary 'Duan, S.' 8 primary 'Allali-Hassani, A.' 9 primary 'Zuo, X.' 10 primary 'Wang, Y.X.' 11 primary 'Bronner, C.' 12 primary 'Chedin, F.' 13 primary 'Arrowsmith, C.H.' 14 primary 'Dhe-Paganon, S.' 15 # _cell.entry_id 3DB3 _cell.length_a 99.622 _cell.length_b 99.622 _cell.length_c 41.232 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 3DB3 _symmetry.space_group_name_H-M 'P 62' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _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 'E3 ubiquitin-protein ligase UHRF1' 19011.543 1 6.3.2.- ? 'Tandem Tudor Domains (UNP residues 126-285)' ? 2 polymer syn 'Trimethylated histone H3-K9 peptide' 706.832 1 ? ? ? ? 3 water nat water 18.015 73 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Ubiquitin-like PHD and RING finger domain-containing protein 1, Ubiquitin-like-containing PHD and RING finger domains protein 1, Inverted CCAAT box-binding protein of 90 kDa, Transcription factor ICBP90, Nuclear zinc finger protein Np95, Nuclear protein 95, HuNp95, RING finger protein 106 ; # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes ;G(MSE)WDETELGLYKVNEYVDARDTN(MSE)GAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGV VQ(MSE)NSRDVRARARTIIKWQDLEVGQVV(MSE)LNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLND CRIIFVDEVFKIERPGE ; ;GMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDV RARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPG E ; A ? 2 'polypeptide(L)' no yes 'TAR(M3L)ST' TARKST B ? # 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 TRP n 1 4 ASP n 1 5 GLU n 1 6 THR n 1 7 GLU n 1 8 LEU n 1 9 GLY n 1 10 LEU n 1 11 TYR n 1 12 LYS n 1 13 VAL n 1 14 ASN n 1 15 GLU n 1 16 TYR n 1 17 VAL n 1 18 ASP n 1 19 ALA n 1 20 ARG n 1 21 ASP n 1 22 THR n 1 23 ASN n 1 24 MSE n 1 25 GLY n 1 26 ALA n 1 27 TRP n 1 28 PHE n 1 29 GLU n 1 30 ALA n 1 31 GLN n 1 32 VAL n 1 33 VAL n 1 34 ARG n 1 35 VAL n 1 36 THR n 1 37 ARG n 1 38 LYS n 1 39 ALA n 1 40 PRO n 1 41 SER n 1 42 ARG n 1 43 ASP n 1 44 GLU n 1 45 PRO n 1 46 CYS n 1 47 SER n 1 48 SER n 1 49 THR n 1 50 SER n 1 51 ARG n 1 52 PRO n 1 53 ALA n 1 54 LEU n 1 55 GLU n 1 56 GLU n 1 57 ASP n 1 58 VAL n 1 59 ILE n 1 60 TYR n 1 61 HIS n 1 62 VAL n 1 63 LYS n 1 64 TYR n 1 65 ASP n 1 66 ASP n 1 67 TYR n 1 68 PRO n 1 69 GLU n 1 70 ASN n 1 71 GLY n 1 72 VAL n 1 73 VAL n 1 74 GLN n 1 75 MSE n 1 76 ASN n 1 77 SER n 1 78 ARG n 1 79 ASP n 1 80 VAL n 1 81 ARG n 1 82 ALA n 1 83 ARG n 1 84 ALA n 1 85 ARG n 1 86 THR n 1 87 ILE n 1 88 ILE n 1 89 LYS n 1 90 TRP n 1 91 GLN n 1 92 ASP n 1 93 LEU n 1 94 GLU n 1 95 VAL n 1 96 GLY n 1 97 GLN n 1 98 VAL n 1 99 VAL n 1 100 MSE n 1 101 LEU n 1 102 ASN n 1 103 TYR n 1 104 ASN n 1 105 PRO n 1 106 ASP n 1 107 ASN n 1 108 PRO n 1 109 LYS n 1 110 GLU n 1 111 ARG n 1 112 GLY n 1 113 PHE n 1 114 TRP n 1 115 TYR n 1 116 ASP n 1 117 ALA n 1 118 GLU n 1 119 ILE n 1 120 SER n 1 121 ARG n 1 122 LYS n 1 123 ARG n 1 124 GLU n 1 125 THR n 1 126 ARG n 1 127 THR n 1 128 ALA n 1 129 ARG n 1 130 GLU n 1 131 LEU n 1 132 TYR n 1 133 ALA n 1 134 ASN n 1 135 VAL n 1 136 VAL n 1 137 LEU n 1 138 GLY n 1 139 ASP n 1 140 ASP n 1 141 SER n 1 142 LEU n 1 143 ASN n 1 144 ASP n 1 145 CYS n 1 146 ARG n 1 147 ILE n 1 148 ILE n 1 149 PHE n 1 150 VAL n 1 151 ASP n 1 152 GLU n 1 153 VAL n 1 154 PHE n 1 155 LYS n 1 156 ILE n 1 157 GLU n 1 158 ARG n 1 159 PRO n 1 160 GLY n 1 161 GLU n 2 1 THR n 2 2 ALA n 2 3 ARG n 2 4 M3L n 2 5 SER n 2 6 THR 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 'UHRF1, ICBP90, NP95, RNF106' _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 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 '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 PET28-MHL _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Trimethylated histone peptide H3-K9 was chemically synthesized. The sequence naturally occurs in Homo sapiens (human)' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP UHRF1_HUMAN Q96T88 1 ;MWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVR ARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGE ; 126 ? 2 UNP H32_HUMAN Q71DI3 2 TARKST 7 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3DB3 A 2 ? 161 ? Q96T88 126 ? 285 ? 126 285 2 2 3DB3 B 1 ? 6 ? Q71DI3 7 ? 12 ? 6 11 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3DB3 _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 Q96T88 _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 125 _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 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 M3L 'L-peptide linking' n N-TRIMETHYLLYSINE ? 'C9 H21 N2 O2 1' 189.275 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.entry_id 3DB3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.00 _exptl_crystal.density_percent_sol 58.94 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.00 _exptl_crystal_grow.pdbx_details '3 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2008-04-09 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'DOUBLE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.99987 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength 0.99987 _diffrn_source.pdbx_wavelength_list 0.99987 # _reflns.entry_id 3DB3 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 32.00 _reflns.d_resolution_high 2.400 _reflns.number_obs 9214 _reflns.number_all 9214 _reflns.percent_possible_obs 98.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.117 _reflns.pdbx_netI_over_sigmaI 22.52 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.9 _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 2.40 _reflns_shell.d_res_low 2.49 _reflns_shell.percent_possible_all 92.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.501 _reflns_shell.meanI_over_sigI_obs 3.62 _reflns_shell.pdbx_redundancy 5.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 852 _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 3DB3 _refine.ls_number_reflns_obs 8755 _refine.ls_number_reflns_all 9124 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 31.77 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 98.50 _refine.ls_R_factor_obs 0.21512 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21188 _refine.ls_R_factor_R_free 0.28198 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 433 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.938 _refine.correlation_coeff_Fo_to_Fc_free 0.886 _refine.B_iso_mean 35.940 _refine.aniso_B[1][1] -3.68 _refine.aniso_B[2][2] -3.68 _refine.aniso_B[3][3] 5.52 _refine.aniso_B[1][2] -1.84 _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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. ; _refine.pdbx_starting_model ? _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 0.296 _refine.pdbx_overall_ESU_R_Free 0.260 _refine.overall_SU_ML 0.195 _refine.overall_SU_B 15.638 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 1164 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 73 _refine_hist.number_atoms_total 1237 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 31.77 # 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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.012 0.022 ? 1184 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.298 1.944 ? 1604 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.481 5.000 ? 140 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38.460 23.538 ? 65 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 17.770 15.000 ? 196 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 19.009 15.000 ? 13 'X-RAY DIFFRACTION' ? r_chiral_restr 0.091 0.200 ? 175 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.020 ? 913 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.205 0.200 ? 424 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.309 0.200 ? 767 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.147 0.200 ? 74 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.158 0.200 ? 14 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.167 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.424 3.000 ? 726 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 2.176 4.000 ? 1144 'X-RAY DIFFRACTION' ? r_scbond_it 3.047 5.000 ? 523 'X-RAY DIFFRACTION' ? r_scangle_it 4.604 7.000 ? 460 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.400 _refine_ls_shell.d_res_low 2.462 _refine_ls_shell.number_reflns_R_work 569 _refine_ls_shell.R_factor_R_work 0.248 _refine_ls_shell.percent_reflns_obs 87.82 _refine_ls_shell.R_factor_R_free 0.223 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _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 3DB3 _struct.title ;Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide ; _struct.pdbx_descriptor 'E3 ubiquitin-protein ligase UHRF1 (E.C.6.3.2.-), Trimethylated histone H3-K9 peptide' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DB3 _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text ;CELL CYCLE, DNA DAMAGE, DNA REPAIR, TANDEM TUDOR DOMAINS, LIGASE, METAL BINDING, DNA REPLICATION, TRANSCRIPTIONAL SILENCING, CHROMATIN, PHOSPHORYLATION, TRANSCRIPTION, TRANSCRIPTION REGULATION, UBL CONJUGATION PATHWAY, ZINC-FINGER, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, DNA-binding, Metal-binding, Nucleus, Phosphoprotein ; # 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 TYR A 67 ? ASN A 70 ? TYR A 191 ASN A 194 5 ? 4 HELX_P HELX_P2 2 LYS A 89 ? LEU A 93 ? LYS A 213 LEU A 217 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 covale1 covale ? ? A ASN 23 C ? ? ? 1_555 A MSE 24 N ? ? A ASN 147 A MSE 148 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale ? ? A MSE 24 C ? ? ? 1_555 A GLY 25 N ? ? A MSE 148 A GLY 149 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale ? ? A GLN 74 C ? ? ? 1_555 A MSE 75 N ? ? A GLN 198 A MSE 199 1_555 ? ? ? ? ? ? ? 1.325 ? covale4 covale ? ? A MSE 75 C ? ? ? 1_555 A ASN 76 N ? ? A MSE 199 A ASN 200 1_555 ? ? ? ? ? ? ? 1.331 ? covale5 covale ? ? A VAL 99 C ? ? ? 1_555 A MSE 100 N ? ? A VAL 223 A MSE 224 1_555 ? ? ? ? ? ? ? 1.337 ? covale6 covale ? ? A MSE 100 C ? ? ? 1_555 A LEU 101 N ? ? A MSE 224 A LEU 225 1_555 ? ? ? ? ? ? ? 1.323 ? covale7 covale ? ? B ARG 3 C ? ? ? 1_555 B M3L 4 N ? ? B ARG 8 B M3L 9 1_555 ? ? ? ? ? ? ? 1.334 ? covale8 covale ? ? B M3L 4 C ? ? ? 1_555 B SER 5 N ? ? B M3L 9 B SER 10 1_555 ? ? ? ? ? ? ? 1.336 ? # _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 ? 5 ? B ? 4 ? # 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 B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 VAL A 72 ? ASN A 76 ? VAL A 196 ASN A 200 A 2 VAL A 58 ? TYR A 64 ? VAL A 182 TYR A 188 A 3 TRP A 27 ? ARG A 37 ? TRP A 151 ARG A 161 A 4 TYR A 16 ? ARG A 20 ? TYR A 140 ARG A 144 A 5 VAL A 80 ? ARG A 81 ? VAL A 204 ARG A 205 B 1 VAL A 98 ? TYR A 103 ? VAL A 222 TYR A 227 B 2 PHE A 113 ? GLU A 124 ? PHE A 237 GLU A 248 B 3 ARG A 129 ? VAL A 136 ? ARG A 253 VAL A 260 B 4 SER A 141 ? ILE A 147 ? SER A 265 ILE A 271 # 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 MSE A 75 ? O MSE A 199 N TYR A 60 ? N TYR A 184 A 2 3 O HIS A 61 ? O HIS A 185 N VAL A 33 ? N VAL A 157 A 3 4 O ALA A 30 ? O ALA A 154 N VAL A 17 ? N VAL A 141 A 4 5 N ASP A 18 ? N ASP A 142 O ARG A 81 ? O ARG A 205 B 1 2 N VAL A 99 ? N VAL A 223 O ALA A 117 ? O ALA A 241 B 2 3 N ARG A 123 ? N ARG A 247 O GLU A 130 ? O GLU A 254 B 3 4 N ALA A 133 ? N ALA A 257 O CYS A 145 ? O CYS A 269 # _database_PDB_matrix.entry_id 3DB3 _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 3DB3 _atom_sites.fract_transf_matrix[1][1] 0.010038 _atom_sites.fract_transf_matrix[1][2] 0.005795 _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] 0.011591 _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] 0.024253 _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 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 1 125 ? ? ? A . n A 1 2 MSE 2 126 ? ? ? A . n A 1 3 TRP 3 127 127 TRP TRP A . n A 1 4 ASP 4 128 128 ASP ASP A . n A 1 5 GLU 5 129 129 GLU GLU A . n A 1 6 THR 6 130 130 THR THR A . n A 1 7 GLU 7 131 131 GLU GLU A . n A 1 8 LEU 8 132 132 LEU LEU A . n A 1 9 GLY 9 133 133 GLY GLY A . n A 1 10 LEU 10 134 134 LEU LEU A . n A 1 11 TYR 11 135 135 TYR TYR A . n A 1 12 LYS 12 136 136 LYS LYS A . n A 1 13 VAL 13 137 137 VAL VAL A . n A 1 14 ASN 14 138 138 ASN ASN A . n A 1 15 GLU 15 139 139 GLU GLU A . n A 1 16 TYR 16 140 140 TYR TYR A . n A 1 17 VAL 17 141 141 VAL VAL A . n A 1 18 ASP 18 142 142 ASP ASP A . n A 1 19 ALA 19 143 143 ALA ALA A . n A 1 20 ARG 20 144 144 ARG ARG A . n A 1 21 ASP 21 145 145 ASP ASP A . n A 1 22 THR 22 146 146 THR THR A . n A 1 23 ASN 23 147 147 ASN ASN A . n A 1 24 MSE 24 148 148 MSE MSE A . n A 1 25 GLY 25 149 149 GLY GLY A . n A 1 26 ALA 26 150 150 ALA ALA A . n A 1 27 TRP 27 151 151 TRP TRP A . n A 1 28 PHE 28 152 152 PHE PHE A . n A 1 29 GLU 29 153 153 GLU GLU A . n A 1 30 ALA 30 154 154 ALA ALA A . n A 1 31 GLN 31 155 155 GLN GLN A . n A 1 32 VAL 32 156 156 VAL VAL A . n A 1 33 VAL 33 157 157 VAL VAL A . n A 1 34 ARG 34 158 158 ARG ARG A . n A 1 35 VAL 35 159 159 VAL VAL A . n A 1 36 THR 36 160 160 THR THR A . n A 1 37 ARG 37 161 161 ARG ARG A . n A 1 38 LYS 38 162 162 LYS LYS A . n A 1 39 ALA 39 163 ? ? ? A . n A 1 40 PRO 40 164 ? ? ? A . n A 1 41 SER 41 165 ? ? ? A . n A 1 42 ARG 42 166 ? ? ? A . n A 1 43 ASP 43 167 ? ? ? A . n A 1 44 GLU 44 168 ? ? ? A . n A 1 45 PRO 45 169 ? ? ? A . n A 1 46 CYS 46 170 ? ? ? A . n A 1 47 SER 47 171 ? ? ? A . n A 1 48 SER 48 172 ? ? ? A . n A 1 49 THR 49 173 ? ? ? A . n A 1 50 SER 50 174 ? ? ? A . n A 1 51 ARG 51 175 ? ? ? A . n A 1 52 PRO 52 176 ? ? ? A . n A 1 53 ALA 53 177 ? ? ? A . n A 1 54 LEU 54 178 ? ? ? A . n A 1 55 GLU 55 179 ? ? ? A . n A 1 56 GLU 56 180 180 GLU GLU A . n A 1 57 ASP 57 181 181 ASP ASP A . n A 1 58 VAL 58 182 182 VAL VAL A . n A 1 59 ILE 59 183 183 ILE ILE A . n A 1 60 TYR 60 184 184 TYR TYR A . n A 1 61 HIS 61 185 185 HIS HIS A . n A 1 62 VAL 62 186 186 VAL VAL A . n A 1 63 LYS 63 187 187 LYS LYS A . n A 1 64 TYR 64 188 188 TYR TYR A . n A 1 65 ASP 65 189 189 ASP ASP A . n A 1 66 ASP 66 190 190 ASP ASP A . n A 1 67 TYR 67 191 191 TYR TYR A . n A 1 68 PRO 68 192 192 PRO PRO A . n A 1 69 GLU 69 193 193 GLU GLU A . n A 1 70 ASN 70 194 194 ASN ASN A . n A 1 71 GLY 71 195 195 GLY GLY A . n A 1 72 VAL 72 196 196 VAL VAL A . n A 1 73 VAL 73 197 197 VAL VAL A . n A 1 74 GLN 74 198 198 GLN GLN A . n A 1 75 MSE 75 199 199 MSE MSE A . n A 1 76 ASN 76 200 200 ASN ASN A . n A 1 77 SER 77 201 201 SER SER A . n A 1 78 ARG 78 202 202 ARG ARG A . n A 1 79 ASP 79 203 203 ASP ASP A . n A 1 80 VAL 80 204 204 VAL VAL A . n A 1 81 ARG 81 205 205 ARG ARG A . n A 1 82 ALA 82 206 206 ALA ALA A . n A 1 83 ARG 83 207 207 ARG ARG A . n A 1 84 ALA 84 208 208 ALA ALA A . n A 1 85 ARG 85 209 209 ARG ARG A . n A 1 86 THR 86 210 210 THR THR A . n A 1 87 ILE 87 211 211 ILE ILE A . n A 1 88 ILE 88 212 212 ILE ILE A . n A 1 89 LYS 89 213 213 LYS LYS A . n A 1 90 TRP 90 214 214 TRP TRP A . n A 1 91 GLN 91 215 215 GLN GLN A . n A 1 92 ASP 92 216 216 ASP ASP A . n A 1 93 LEU 93 217 217 LEU LEU A . n A 1 94 GLU 94 218 218 GLU GLU A . n A 1 95 VAL 95 219 219 VAL VAL A . n A 1 96 GLY 96 220 220 GLY GLY A . n A 1 97 GLN 97 221 221 GLN GLN A . n A 1 98 VAL 98 222 222 VAL VAL A . n A 1 99 VAL 99 223 223 VAL VAL A . n A 1 100 MSE 100 224 224 MSE MSE A . n A 1 101 LEU 101 225 225 LEU LEU A . n A 1 102 ASN 102 226 226 ASN ASN A . n A 1 103 TYR 103 227 227 TYR TYR A . n A 1 104 ASN 104 228 228 ASN ASN A . n A 1 105 PRO 105 229 229 PRO PRO A . n A 1 106 ASP 106 230 230 ASP ASP A . n A 1 107 ASN 107 231 231 ASN ASN A . n A 1 108 PRO 108 232 232 PRO PRO A . n A 1 109 LYS 109 233 233 LYS LYS A . n A 1 110 GLU 110 234 234 GLU GLU A . n A 1 111 ARG 111 235 235 ARG ARG A . n A 1 112 GLY 112 236 236 GLY GLY A . n A 1 113 PHE 113 237 237 PHE PHE A . n A 1 114 TRP 114 238 238 TRP TRP A . n A 1 115 TYR 115 239 239 TYR TYR A . n A 1 116 ASP 116 240 240 ASP ASP A . n A 1 117 ALA 117 241 241 ALA ALA A . n A 1 118 GLU 118 242 242 GLU GLU A . n A 1 119 ILE 119 243 243 ILE ILE A . n A 1 120 SER 120 244 244 SER SER A . n A 1 121 ARG 121 245 245 ARG ARG A . n A 1 122 LYS 122 246 246 LYS LYS A . n A 1 123 ARG 123 247 247 ARG ARG A . n A 1 124 GLU 124 248 248 GLU GLU A . n A 1 125 THR 125 249 249 THR THR A . n A 1 126 ARG 126 250 250 ARG ARG A . n A 1 127 THR 127 251 251 THR THR A . n A 1 128 ALA 128 252 252 ALA ALA A . n A 1 129 ARG 129 253 253 ARG ARG A . n A 1 130 GLU 130 254 254 GLU GLU A . n A 1 131 LEU 131 255 255 LEU LEU A . n A 1 132 TYR 132 256 256 TYR TYR A . n A 1 133 ALA 133 257 257 ALA ALA A . n A 1 134 ASN 134 258 258 ASN ASN A . n A 1 135 VAL 135 259 259 VAL VAL A . n A 1 136 VAL 136 260 260 VAL VAL A . n A 1 137 LEU 137 261 261 LEU LEU A . n A 1 138 GLY 138 262 262 GLY GLY A . n A 1 139 ASP 139 263 263 ASP ASP A . n A 1 140 ASP 140 264 264 ASP ASP A . n A 1 141 SER 141 265 265 SER SER A . n A 1 142 LEU 142 266 266 LEU LEU A . n A 1 143 ASN 143 267 267 ASN ASN A . n A 1 144 ASP 144 268 268 ASP ASP A . n A 1 145 CYS 145 269 269 CYS CYS A . n A 1 146 ARG 146 270 270 ARG ARG A . n A 1 147 ILE 147 271 271 ILE ILE A . n A 1 148 ILE 148 272 272 ILE ILE A . n A 1 149 PHE 149 273 273 PHE PHE A . n A 1 150 VAL 150 274 274 VAL VAL A . n A 1 151 ASP 151 275 275 ASP ASP A . n A 1 152 GLU 152 276 276 GLU GLU A . n A 1 153 VAL 153 277 277 VAL VAL A . n A 1 154 PHE 154 278 278 PHE PHE A . n A 1 155 LYS 155 279 279 LYS LYS A . n A 1 156 ILE 156 280 280 ILE ILE A . n A 1 157 GLU 157 281 281 GLU GLU A . n A 1 158 ARG 158 282 282 ARG ARG A . n A 1 159 PRO 159 283 283 PRO PRO A . n A 1 160 GLY 160 284 ? ? ? A . n A 1 161 GLU 161 285 ? ? ? A . n B 2 1 THR 1 6 ? ? ? B . n B 2 2 ALA 2 7 ? ? ? B . n B 2 3 ARG 3 8 8 ARG ARG B . n B 2 4 M3L 4 9 9 M3L M3L B . n B 2 5 SER 5 10 10 SER SER B . n B 2 6 THR 6 11 ? ? ? B . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'Structural Genomics Consortium' _pdbx_SG_project.initial_of_center SGC # 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 C 3 HOH 1 301 301 HOH HOH A . C 3 HOH 2 302 302 HOH HOH A . C 3 HOH 3 303 303 HOH HOH A . C 3 HOH 4 304 304 HOH HOH A . C 3 HOH 5 305 305 HOH HOH A . C 3 HOH 6 306 306 HOH HOH A . C 3 HOH 7 307 307 HOH HOH A . C 3 HOH 8 308 308 HOH HOH A . C 3 HOH 9 309 309 HOH HOH A . C 3 HOH 10 310 310 HOH HOH A . C 3 HOH 11 311 311 HOH HOH A . C 3 HOH 12 312 312 HOH HOH A . C 3 HOH 13 313 313 HOH HOH A . C 3 HOH 14 314 314 HOH HOH A . C 3 HOH 15 315 315 HOH HOH A . C 3 HOH 16 316 316 HOH HOH A . C 3 HOH 17 317 317 HOH HOH A . C 3 HOH 18 318 318 HOH HOH A . C 3 HOH 19 319 319 HOH HOH A . C 3 HOH 20 320 320 HOH HOH A . C 3 HOH 21 321 321 HOH HOH A . C 3 HOH 22 322 322 HOH HOH A . C 3 HOH 23 323 323 HOH HOH A . C 3 HOH 24 324 324 HOH HOH A . C 3 HOH 25 325 325 HOH HOH A . C 3 HOH 26 326 326 HOH HOH A . C 3 HOH 27 327 327 HOH HOH A . C 3 HOH 28 328 328 HOH HOH A . C 3 HOH 29 329 329 HOH HOH A . C 3 HOH 30 330 330 HOH HOH A . C 3 HOH 31 331 331 HOH HOH A . C 3 HOH 32 332 332 HOH HOH A . C 3 HOH 33 333 333 HOH HOH A . C 3 HOH 34 334 334 HOH HOH A . C 3 HOH 35 335 335 HOH HOH A . C 3 HOH 36 336 336 HOH HOH A . C 3 HOH 37 337 337 HOH HOH A . C 3 HOH 38 338 338 HOH HOH A . C 3 HOH 39 339 339 HOH HOH A . C 3 HOH 40 340 340 HOH HOH A . C 3 HOH 41 341 341 HOH HOH A . C 3 HOH 42 342 342 HOH HOH A . C 3 HOH 43 343 343 HOH HOH A . C 3 HOH 44 344 344 HOH HOH A . C 3 HOH 45 345 345 HOH HOH A . C 3 HOH 46 346 346 HOH HOH A . C 3 HOH 47 347 347 HOH HOH A . C 3 HOH 48 348 348 HOH HOH A . C 3 HOH 49 349 349 HOH HOH A . C 3 HOH 50 350 350 HOH HOH A . C 3 HOH 51 351 351 HOH HOH A . C 3 HOH 52 352 352 HOH HOH A . C 3 HOH 53 353 353 HOH HOH A . C 3 HOH 54 354 354 HOH HOH A . C 3 HOH 55 356 356 HOH HOH A . C 3 HOH 56 357 357 HOH HOH A . C 3 HOH 57 358 358 HOH HOH A . C 3 HOH 58 359 359 HOH HOH A . C 3 HOH 59 360 360 HOH HOH A . C 3 HOH 60 361 361 HOH HOH A . C 3 HOH 61 362 362 HOH HOH A . C 3 HOH 62 363 363 HOH HOH A . C 3 HOH 63 364 364 HOH HOH A . C 3 HOH 64 365 365 HOH HOH A . C 3 HOH 65 366 366 HOH HOH A . C 3 HOH 66 367 367 HOH HOH A . C 3 HOH 67 368 368 HOH HOH A . C 3 HOH 68 369 369 HOH HOH A . C 3 HOH 69 370 370 HOH HOH A . C 3 HOH 70 371 371 HOH HOH A . C 3 HOH 71 372 372 HOH HOH A . C 3 HOH 72 373 373 HOH HOH A . C 3 HOH 73 374 374 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 24 A MSE 148 ? MET SELENOMETHIONINE 2 A MSE 75 A MSE 199 ? MET SELENOMETHIONINE 3 A MSE 100 A MSE 224 ? MET SELENOMETHIONINE 4 B M3L 4 B M3L 9 ? LYS N-TRIMETHYLLYSINE # _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 _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)' 530 ? 1 MORE -6.4 ? 1 'SSA (A^2)' 8640 ? # _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 2008-09-16 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-04-18 # _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 ? # 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' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.pdbx_refine_id 1 ? refined 28.0556 -0.6752 20.5866 0.2682 -0.0187 0.0335 0.0275 0.0737 -0.1192 2.4227 42.3760 3.0403 5.7516 0.5587 -7.8179 -0.7935 -0.8142 0.2144 1.4510 1.0206 2.7258 -0.6698 -0.1124 -0.2271 'X-RAY DIFFRACTION' 2 ? refined 33.0352 -6.6195 7.8505 -0.0064 0.0356 0.2101 0.0188 0.0166 -0.0549 4.1551 6.8888 21.7632 1.2594 4.8994 5.9467 0.2137 -0.0139 0.1202 -0.0331 -0.1573 0.2263 0.1832 -0.3221 -0.0564 'X-RAY DIFFRACTION' 3 ? refined 32.4740 -3.1657 12.0750 0.1437 -0.0196 0.0160 0.0099 -0.0075 0.0131 3.8692 11.2789 9.5482 0.3710 -3.0512 5.4679 0.4256 -0.1986 0.3873 0.3700 -0.0336 -0.0255 -0.3589 -0.1399 -0.3920 'X-RAY DIFFRACTION' 4 ? refined 33.4396 -0.2793 9.5177 0.0819 0.0186 0.1620 0.0019 -0.0030 -0.0804 8.3427 5.9341 9.6671 -1.8807 -5.2850 0.5944 0.0145 0.1132 -0.6022 0.1757 -0.1031 0.2898 -0.0301 -0.4058 0.0886 'X-RAY DIFFRACTION' 5 ? refined 33.4613 -18.4890 8.7983 0.2462 0.0430 0.0905 0.0279 -0.0463 -0.0397 3.0946 4.8554 1.5442 2.3640 0.0699 2.2223 0.1010 -0.2008 -0.1076 0.5993 0.0643 -0.0475 0.1797 0.0606 -0.1653 'X-RAY DIFFRACTION' 6 ? refined 33.2903 -20.4219 -3.1923 0.0780 0.0795 0.0927 0.0049 -0.0624 -0.0336 5.1187 4.8493 4.3799 -0.2452 -0.4938 1.3318 0.0701 0.2857 0.0196 -0.1337 -0.0298 -0.0484 -0.2041 0.0792 -0.0402 'X-RAY DIFFRACTION' 7 ? refined 35.5952 -32.8890 -7.2742 0.0438 0.0580 0.1736 -0.0466 -0.0412 -0.0936 4.9679 15.3126 2.4486 -8.2626 -3.0329 4.0760 0.0105 0.2433 -0.2258 -0.4986 -0.2006 -0.0044 -0.0290 -0.0509 0.1901 'X-RAY DIFFRACTION' 8 ? refined 31.6191 -20.0237 -0.4756 0.0980 0.0904 0.1245 -0.0721 -0.0022 -0.0472 4.5652 5.2364 8.1511 -0.6866 1.0698 1.9592 -0.0230 0.0775 0.1244 -0.1184 -0.1095 0.0842 -0.2454 -0.4368 0.1325 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 127 A 3 A 137 A 13 ? 'X-RAY DIFFRACTION' ? 2 2 A 138 A 14 A 149 A 25 ? 'X-RAY DIFFRACTION' ? 3 3 A 150 A 26 A 162 A 38 ? 'X-RAY DIFFRACTION' ? 4 4 A 180 A 56 A 198 A 74 ? 'X-RAY DIFFRACTION' ? 5 5 A 199 A 75 A 216 A 92 ? 'X-RAY DIFFRACTION' ? 6 6 A 217 A 93 A 246 A 122 ? 'X-RAY DIFFRACTION' ? 7 7 A 247 A 123 A 258 A 134 ? 'X-RAY DIFFRACTION' ? 8 8 A 259 A 135 A 283 A 159 ? 'X-RAY DIFFRACTION' ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 HKL-3000 'data collection' . ? 2 HKL-3000 'data reduction' . ? 3 HKL-3000 'data scaling' . ? 4 REFMAC phasing 5.2.0019 ? 5 # 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 GLU A 129 ? ? -112.29 56.05 2 1 ASN A 138 ? ? 91.15 -1.77 3 1 THR A 249 ? ? -110.84 -168.41 # 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 TRP 127 ? CG ? A TRP 3 CG 2 1 Y 1 A TRP 127 ? CD1 ? A TRP 3 CD1 3 1 Y 1 A TRP 127 ? CD2 ? A TRP 3 CD2 4 1 Y 1 A TRP 127 ? NE1 ? A TRP 3 NE1 5 1 Y 1 A TRP 127 ? CE2 ? A TRP 3 CE2 6 1 Y 1 A TRP 127 ? CE3 ? A TRP 3 CE3 7 1 Y 1 A TRP 127 ? CZ2 ? A TRP 3 CZ2 8 1 Y 1 A TRP 127 ? CZ3 ? A TRP 3 CZ3 9 1 Y 1 A TRP 127 ? CH2 ? A TRP 3 CH2 10 1 Y 1 A GLU 129 ? CG ? A GLU 5 CG 11 1 Y 1 A GLU 129 ? CD ? A GLU 5 CD 12 1 Y 1 A GLU 129 ? OE1 ? A GLU 5 OE1 13 1 Y 1 A GLU 129 ? OE2 ? A GLU 5 OE2 14 1 Y 1 A GLU 131 ? CG ? A GLU 7 CG 15 1 Y 1 A GLU 131 ? CD ? A GLU 7 CD 16 1 Y 1 A GLU 131 ? OE1 ? A GLU 7 OE1 17 1 Y 1 A GLU 131 ? OE2 ? A GLU 7 OE2 18 1 Y 1 A LYS 136 ? CE ? A LYS 12 CE 19 1 Y 1 A LYS 136 ? NZ ? A LYS 12 NZ 20 1 Y 1 A ARG 161 ? CG ? A ARG 37 CG 21 1 Y 1 A ARG 161 ? CD ? A ARG 37 CD 22 1 Y 1 A ARG 161 ? NE ? A ARG 37 NE 23 1 Y 1 A ARG 161 ? CZ ? A ARG 37 CZ 24 1 Y 1 A ARG 161 ? NH1 ? A ARG 37 NH1 25 1 Y 1 A ARG 161 ? NH2 ? A ARG 37 NH2 26 1 Y 1 A LYS 162 ? CG ? A LYS 38 CG 27 1 Y 1 A LYS 162 ? CD ? A LYS 38 CD 28 1 Y 1 A LYS 162 ? CE ? A LYS 38 CE 29 1 Y 1 A LYS 162 ? NZ ? A LYS 38 NZ 30 1 Y 1 A ASP 181 ? CG ? A ASP 57 CG 31 1 Y 1 A ASP 181 ? OD1 ? A ASP 57 OD1 32 1 Y 1 A ASP 181 ? OD2 ? A ASP 57 OD2 33 1 Y 1 A ARG 202 ? CZ ? A ARG 78 CZ 34 1 Y 1 A ARG 202 ? NH1 ? A ARG 78 NH1 35 1 Y 1 A ARG 202 ? NH2 ? A ARG 78 NH2 36 1 Y 1 A ASP 263 ? CG ? A ASP 139 CG 37 1 Y 1 A ASP 263 ? OD1 ? A ASP 139 OD1 38 1 Y 1 A ASP 263 ? OD2 ? A ASP 139 OD2 # 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 125 ? A GLY 1 2 1 Y 1 A MSE 126 ? A MSE 2 3 1 Y 1 A ALA 163 ? A ALA 39 4 1 Y 1 A PRO 164 ? A PRO 40 5 1 Y 1 A SER 165 ? A SER 41 6 1 Y 1 A ARG 166 ? A ARG 42 7 1 Y 1 A ASP 167 ? A ASP 43 8 1 Y 1 A GLU 168 ? A GLU 44 9 1 Y 1 A PRO 169 ? A PRO 45 10 1 Y 1 A CYS 170 ? A CYS 46 11 1 Y 1 A SER 171 ? A SER 47 12 1 Y 1 A SER 172 ? A SER 48 13 1 Y 1 A THR 173 ? A THR 49 14 1 Y 1 A SER 174 ? A SER 50 15 1 Y 1 A ARG 175 ? A ARG 51 16 1 Y 1 A PRO 176 ? A PRO 52 17 1 Y 1 A ALA 177 ? A ALA 53 18 1 Y 1 A LEU 178 ? A LEU 54 19 1 Y 1 A GLU 179 ? A GLU 55 20 1 Y 1 A GLY 284 ? A GLY 160 21 1 Y 1 A GLU 285 ? A GLU 161 22 1 Y 1 B THR 6 ? B THR 1 23 1 Y 1 B ALA 7 ? B ALA 2 24 1 Y 1 B THR 11 ? B THR 6 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #