data_1UMH # _entry.id 1UMH # _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 1UMH RCSB RCSB005990 WWPDB D_1000005990 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1UMI '1UMI contains the same protein complexed with sugar' unspecified TargetDB trt001000323.1 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1UMH _pdbx_database_status.recvd_initial_deposition_date 2003-10-01 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mizushima, T.' 1 'Hirao, T.' 2 'Yoshida, Y.' 3 'Lee, S.J.' 4 'Chiba, T.' 5 'Iwai, K.' 6 'Yamaguchi, Y.' 7 'Kato, K.' 8 'Tsukihara, T.' 9 'Tanaka, K.' 10 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 11 # _citation.id primary _citation.title 'Structural basis of sugar-recognizing ubiquitin ligase' _citation.journal_abbrev NAT.STRUCT.MOL.BIOL. _citation.journal_volume 11 _citation.page_first 365 _citation.page_last 370 _citation.year 2004 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14990996 _citation.pdbx_database_id_DOI 10.1038/nsmb732 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Mizushima, T.' 1 primary 'Hirao, T.' 2 primary 'Yoshida, Y.' 3 primary 'Lee, S.J.' 4 primary 'Chiba, T.' 5 primary 'Iwai, K.' 6 primary 'Yamaguchi, Y.' 7 primary 'Kato, K.' 8 primary 'Tsukihara, T.' 9 primary 'Tanaka, K.' 10 # _cell.entry_id 1UMH _cell.length_a 62.440 _cell.length_b 62.440 _cell.length_c 117.300 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1UMH _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 # 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 'F-box only protein 2' 21021.010 1 6.3.2.19 ? 'SBD DOMAIN' ? 2 non-polymer syn 'NICKEL (II) ION' 58.693 1 ? ? ? ? 3 water nat water 18.015 112 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Fbs1 # _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 ;GSHFYFLSKRRRNLLRNPCGEEDLEGWSDVEHGGDGWKVEELPGDNGVEFTQDDSVKKYFASSFEWCRKAQVIDLQAEGY WEELLDTTQPAIVVKDWYSGRTDAGSLYELTVRLLSENEDVLAEFATGQVAVPEDGSWMEISHTFIDYGPGVRFVRFEHG GQDSVYWKGWFGARVTNSSVWVEP ; _entity_poly.pdbx_seq_one_letter_code_can ;GSHFYFLSKRRRNLLRNPCGEEDLEGWSDVEHGGDGWKVEELPGDNGVEFTQDDSVKKYFASSFEWCRKAQVIDLQAEGY WEELLDTTQPAIVVKDWYSGRTDAGSLYELTVRLLSENEDVLAEFATGQVAVPEDGSWMEISHTFIDYGPGVRFVRFEHG GQDSVYWKGWFGARVTNSSVWVEP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier trt001000323.1 # 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 SER n 1 3 HIS n 1 4 PHE n 1 5 TYR n 1 6 PHE n 1 7 LEU n 1 8 SER n 1 9 LYS n 1 10 ARG n 1 11 ARG n 1 12 ARG n 1 13 ASN n 1 14 LEU n 1 15 LEU n 1 16 ARG n 1 17 ASN n 1 18 PRO n 1 19 CYS n 1 20 GLY n 1 21 GLU n 1 22 GLU n 1 23 ASP n 1 24 LEU n 1 25 GLU n 1 26 GLY n 1 27 TRP n 1 28 SER n 1 29 ASP n 1 30 VAL n 1 31 GLU n 1 32 HIS n 1 33 GLY n 1 34 GLY n 1 35 ASP n 1 36 GLY n 1 37 TRP n 1 38 LYS n 1 39 VAL n 1 40 GLU n 1 41 GLU n 1 42 LEU n 1 43 PRO n 1 44 GLY n 1 45 ASP n 1 46 ASN n 1 47 GLY n 1 48 VAL n 1 49 GLU n 1 50 PHE n 1 51 THR n 1 52 GLN n 1 53 ASP n 1 54 ASP n 1 55 SER n 1 56 VAL n 1 57 LYS n 1 58 LYS n 1 59 TYR n 1 60 PHE n 1 61 ALA n 1 62 SER n 1 63 SER n 1 64 PHE n 1 65 GLU n 1 66 TRP n 1 67 CYS n 1 68 ARG n 1 69 LYS n 1 70 ALA n 1 71 GLN n 1 72 VAL n 1 73 ILE n 1 74 ASP n 1 75 LEU n 1 76 GLN n 1 77 ALA n 1 78 GLU n 1 79 GLY n 1 80 TYR n 1 81 TRP n 1 82 GLU n 1 83 GLU n 1 84 LEU n 1 85 LEU n 1 86 ASP n 1 87 THR n 1 88 THR n 1 89 GLN n 1 90 PRO n 1 91 ALA n 1 92 ILE n 1 93 VAL n 1 94 VAL n 1 95 LYS n 1 96 ASP n 1 97 TRP n 1 98 TYR n 1 99 SER n 1 100 GLY n 1 101 ARG n 1 102 THR n 1 103 ASP n 1 104 ALA n 1 105 GLY n 1 106 SER n 1 107 LEU n 1 108 TYR n 1 109 GLU n 1 110 LEU n 1 111 THR n 1 112 VAL n 1 113 ARG n 1 114 LEU n 1 115 LEU n 1 116 SER n 1 117 GLU n 1 118 ASN n 1 119 GLU n 1 120 ASP n 1 121 VAL n 1 122 LEU n 1 123 ALA n 1 124 GLU n 1 125 PHE n 1 126 ALA n 1 127 THR n 1 128 GLY n 1 129 GLN n 1 130 VAL n 1 131 ALA n 1 132 VAL n 1 133 PRO n 1 134 GLU n 1 135 ASP n 1 136 GLY n 1 137 SER n 1 138 TRP n 1 139 MET n 1 140 GLU n 1 141 ILE n 1 142 SER n 1 143 HIS n 1 144 THR n 1 145 PHE n 1 146 ILE n 1 147 ASP n 1 148 TYR n 1 149 GLY n 1 150 PRO n 1 151 GLY n 1 152 VAL n 1 153 ARG n 1 154 PHE n 1 155 VAL n 1 156 ARG n 1 157 PHE n 1 158 GLU n 1 159 HIS n 1 160 GLY n 1 161 GLY n 1 162 GLN n 1 163 ASP n 1 164 SER n 1 165 VAL n 1 166 TYR n 1 167 TRP n 1 168 LYS n 1 169 GLY n 1 170 TRP n 1 171 PHE n 1 172 GLY n 1 173 ALA n 1 174 ARG n 1 175 VAL n 1 176 THR n 1 177 ASN n 1 178 SER n 1 179 SER n 1 180 VAL n 1 181 TRP n 1 182 VAL n 1 183 GLU n 1 184 PRO 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 'house mouse' _entity_src_gen.gene_src_genus Mus _entity_src_gen.pdbx_gene_src_gene mouse _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 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species 'Escherichia coli' _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 pET15b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code FBX2_MOUSE _struct_ref.pdbx_db_accession Q80UW2 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;FYFLSKRRRNLLRNPCGEEDLEGWSDVEHGGDGWRVEELPGDNGVEFTQDDSVKKYFASSFEWCRKAQVIDLQAEGYWEE LLDTTQPAIVVKDWYSGRTDAGSLYELTVRLLSENEDVLAEFATGQVAVPEDGSWMEISHTFIDYGPGVRFVRFEHGGQD SVYWKGWFGARVTNSSVWVEP ; _struct_ref.pdbx_align_begin 117 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1UMH _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 184 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q80UW2 _struct_ref_seq.db_align_beg 117 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 297 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 117 _struct_ref_seq.pdbx_auth_seq_align_end 297 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1UMH GLY A 1 ? UNP Q80UW2 ? ? 'CLONING ARTIFACT' 114 1 1 1UMH SER A 2 ? UNP Q80UW2 ? ? 'CLONING ARTIFACT' 115 2 1 1UMH HIS A 3 ? UNP Q80UW2 ? ? 'CLONING ARTIFACT' 116 3 1 1UMH LYS A 38 ? UNP Q80UW2 ARG 151 'SEE REMARK 999' 151 4 # 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 NI non-polymer . 'NICKEL (II) ION' ? 'Ni 2' 58.693 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 1UMH _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.14 _exptl_crystal.density_percent_sol 60.82 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_details 'Tris, PEG400, Nickel Chloride, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2002-09-20 _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 'YALE MIRRORS' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1UMH _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 2.0 _reflns.d_resolution_low 100 _reflns.number_all 18483 _reflns.number_obs 18483 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2 _reflns_shell.d_res_low 2.11 _reflns_shell.percent_possible_all 99.9 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.278 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 10.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 2647 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1UMH _refine.ls_number_reflns_obs 17470 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 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 54.23 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 99.64 _refine.ls_R_factor_obs 0.15523 _refine.ls_R_factor_all 0.15523 _refine.ls_R_factor_R_work 0.15327 _refine.ls_R_factor_R_free 0.19229 _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 945 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.971 _refine.correlation_coeff_Fo_to_Fc_free 0.956 _refine.B_iso_mean 29.192 _refine.aniso_B[1][1] -0.36 _refine.aniso_B[2][2] -0.36 _refine.aniso_B[3][3] 0.54 _refine.aniso_B[1][2] -0.18 _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 1.40 _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 ? _refine.pdbx_method_to_determine_struct MIR _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 0.119 _refine.pdbx_overall_ESU_R_Free 0.119 _refine.overall_SU_ML 0.077 _refine.overall_SU_B 2.720 _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1489 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 112 _refine_hist.number_atoms_total 1602 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 54.23 # 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 0.022 0.021 ? 1533 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1290 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.785 1.912 ? 2082 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.964 3.000 ? 2996 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.955 5.000 ? 183 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.127 0.200 ? 207 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 1757 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 348 'X-RAY DIFFRACTION' ? r_nbd_refined 0.232 0.200 ? 222 'X-RAY DIFFRACTION' ? r_nbd_other 0.274 0.200 ? 1420 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other 0.089 0.200 ? 904 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.178 0.200 ? 64 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.158 0.200 ? 1 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.090 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.297 0.200 ? 30 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.334 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1.354 1.500 ? 907 'X-RAY DIFFRACTION' ? r_mcangle_it 2.585 2.000 ? 1451 'X-RAY DIFFRACTION' ? r_scbond_it 4.061 3.000 ? 626 'X-RAY DIFFRACTION' ? r_scangle_it 6.651 4.500 ? 631 '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 2.001 _refine_ls_shell.d_res_low 2.053 _refine_ls_shell.number_reflns_R_work 1241 _refine_ls_shell.R_factor_R_work 0.183 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.241 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 74 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 1UMH _struct.title 'Structural basis of sugar-recognizing ubiquitin ligase' _struct.pdbx_descriptor 'F-box only protein 2(E.C.6.3.2.19)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1UMH _struct_keywords.pdbx_keywords LIGASE _struct_keywords.text 'UBIQUITIN, SCF, UBIQUITIN LIGASE, LECTIN, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, LIGASE' # 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 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 2 ? ARG A 10 ? SER A 115 ARG A 123 1 ? 9 HELX_P HELX_P2 2 TRP A 81 ? THR A 88 ? TRP A 194 THR A 201 1 ? 8 # _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 metalc1 metalc ? ? B NI . NI ? ? ? 1_555 A GLY 1 N ? ? A NI 501 A GLY 114 1_555 ? ? ? ? ? ? ? 2.052 ? metalc2 metalc ? ? B NI . NI ? ? ? 1_555 A SER 2 OG ? ? A NI 501 A SER 115 1_555 ? ? ? ? ? ? ? 2.198 ? metalc3 metalc ? ? B NI . NI ? ? ? 1_555 A SER 2 N ? ? A NI 501 A SER 115 1_555 ? ? ? ? ? ? ? 1.791 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id LEU _struct_mon_prot_cis.label_seq_id 42 _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 LEU _struct_mon_prot_cis.auth_seq_id 155 _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 43 _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_2 156 _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 -10.23 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 5 ? C ? 5 ? # 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 B 4 5 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel C 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 SER A 28 ? GLU A 31 ? SER A 141 GLU A 144 A 2 CYS A 67 ? ASP A 74 ? CYS A 180 ASP A 187 A 3 PHE A 154 ? ASP A 163 ? PHE A 267 ASP A 276 A 4 SER A 106 ? LEU A 115 ? SER A 219 LEU A 228 A 5 VAL A 121 ? ALA A 126 ? VAL A 234 ALA A 239 B 1 SER A 28 ? GLU A 31 ? SER A 141 GLU A 144 B 2 CYS A 67 ? ASP A 74 ? CYS A 180 ASP A 187 B 3 PHE A 154 ? ASP A 163 ? PHE A 267 ASP A 276 B 4 SER A 106 ? LEU A 115 ? SER A 219 LEU A 228 B 5 VAL A 130 ? ALA A 131 ? VAL A 243 ALA A 244 C 1 LYS A 38 ? GLU A 41 ? LYS A 151 GLU A 154 C 2 LYS A 58 ? ALA A 61 ? LYS A 171 ALA A 174 C 3 ARG A 174 ? GLU A 183 ? ARG A 287 GLU A 296 C 4 ALA A 91 ? SER A 99 ? ALA A 204 SER A 212 C 5 MET A 139 ? PHE A 145 ? MET A 252 PHE A 258 # 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 SER A 28 ? N SER A 141 O ALA A 70 ? O ALA A 183 A 2 3 N ILE A 73 ? N ILE A 186 O VAL A 155 ? O VAL A 268 A 3 4 O GLN A 162 ? O GLN A 275 N LEU A 107 ? N LEU A 220 A 4 5 N VAL A 112 ? N VAL A 225 O PHE A 125 ? O PHE A 238 B 1 2 N SER A 28 ? N SER A 141 O ALA A 70 ? O ALA A 183 B 2 3 N ILE A 73 ? N ILE A 186 O VAL A 155 ? O VAL A 268 B 3 4 O GLN A 162 ? O GLN A 275 N LEU A 107 ? N LEU A 220 B 4 5 N TYR A 108 ? N TYR A 221 O VAL A 130 ? O VAL A 243 C 1 2 N LYS A 38 ? N LYS A 151 O ALA A 61 ? O ALA A 174 C 2 3 N PHE A 60 ? N PHE A 173 O VAL A 175 ? O VAL A 288 C 3 4 O ARG A 174 ? O ARG A 287 N SER A 99 ? N SER A 212 C 4 5 N ILE A 92 ? N ILE A 205 O PHE A 145 ? O PHE A 258 # _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 3 _struct_site.details 'BINDING SITE FOR RESIDUE NI A 501' # 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 3 GLY A 1 ? GLY A 114 . ? 1_555 ? 2 AC1 3 SER A 2 ? SER A 115 . ? 1_555 ? 3 AC1 3 TYR A 5 ? TYR A 118 . ? 1_555 ? # _database_PDB_matrix.entry_id 1UMH _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 1UMH _atom_sites.fract_transf_matrix[1][1] 0.016015 _atom_sites.fract_transf_matrix[1][2] 0.009246 _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] 0.018493 _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] 0.008525 _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 NI O 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 GLY 1 114 114 GLY GLY A . n A 1 2 SER 2 115 115 SER SER A . n A 1 3 HIS 3 116 116 HIS HIS A . n A 1 4 PHE 4 117 117 PHE PHE A . n A 1 5 TYR 5 118 118 TYR TYR A . n A 1 6 PHE 6 119 119 PHE PHE A . n A 1 7 LEU 7 120 120 LEU LEU A . n A 1 8 SER 8 121 121 SER SER A . n A 1 9 LYS 9 122 122 LYS LYS A . n A 1 10 ARG 10 123 123 ARG ARG A . n A 1 11 ARG 11 124 124 ARG ARG A . n A 1 12 ARG 12 125 125 ARG ARG A . n A 1 13 ASN 13 126 126 ASN ASN A . n A 1 14 LEU 14 127 127 LEU LEU A . n A 1 15 LEU 15 128 128 LEU LEU A . n A 1 16 ARG 16 129 129 ARG ARG A . n A 1 17 ASN 17 130 130 ASN ASN A . n A 1 18 PRO 18 131 131 PRO PRO A . n A 1 19 CYS 19 132 132 CYS CYS A . n A 1 20 GLY 20 133 133 GLY GLY A . n A 1 21 GLU 21 134 134 GLU GLU A . n A 1 22 GLU 22 135 135 GLU GLU A . n A 1 23 ASP 23 136 136 ASP ASP A . n A 1 24 LEU 24 137 137 LEU LEU A . n A 1 25 GLU 25 138 138 GLU GLU A . n A 1 26 GLY 26 139 139 GLY GLY A . n A 1 27 TRP 27 140 140 TRP TRP A . n A 1 28 SER 28 141 141 SER SER A . n A 1 29 ASP 29 142 142 ASP ASP A . n A 1 30 VAL 30 143 143 VAL VAL A . n A 1 31 GLU 31 144 144 GLU GLU A . n A 1 32 HIS 32 145 145 HIS HIS A . n A 1 33 GLY 33 146 146 GLY GLY A . n A 1 34 GLY 34 147 147 GLY GLY A . n A 1 35 ASP 35 148 148 ASP ASP A . n A 1 36 GLY 36 149 149 GLY GLY A . n A 1 37 TRP 37 150 150 TRP TRP A . n A 1 38 LYS 38 151 151 LYS LYS A . n A 1 39 VAL 39 152 152 VAL VAL A . n A 1 40 GLU 40 153 153 GLU GLU A . n A 1 41 GLU 41 154 154 GLU GLU A . n A 1 42 LEU 42 155 155 LEU LEU A . n A 1 43 PRO 43 156 156 PRO PRO A . n A 1 44 GLY 44 157 157 GLY GLY A . n A 1 45 ASP 45 158 158 ASP ASP A . n A 1 46 ASN 46 159 159 ASN ASN A . n A 1 47 GLY 47 160 160 GLY GLY A . n A 1 48 VAL 48 161 161 VAL VAL A . n A 1 49 GLU 49 162 162 GLU GLU A . n A 1 50 PHE 50 163 163 PHE PHE A . n A 1 51 THR 51 164 164 THR THR A . n A 1 52 GLN 52 165 165 GLN GLN A . n A 1 53 ASP 53 166 166 ASP ASP A . n A 1 54 ASP 54 167 167 ASP ASP A . n A 1 55 SER 55 168 168 SER SER A . n A 1 56 VAL 56 169 169 VAL VAL A . n A 1 57 LYS 57 170 170 LYS LYS A . n A 1 58 LYS 58 171 171 LYS LYS A . n A 1 59 TYR 59 172 172 TYR TYR A . n A 1 60 PHE 60 173 173 PHE PHE A . n A 1 61 ALA 61 174 174 ALA ALA A . n A 1 62 SER 62 175 175 SER SER A . n A 1 63 SER 63 176 176 SER SER A . n A 1 64 PHE 64 177 177 PHE PHE A . n A 1 65 GLU 65 178 178 GLU GLU A . n A 1 66 TRP 66 179 179 TRP TRP A . n A 1 67 CYS 67 180 180 CYS CYS A . n A 1 68 ARG 68 181 181 ARG ARG A . n A 1 69 LYS 69 182 182 LYS LYS A . n A 1 70 ALA 70 183 183 ALA ALA A . n A 1 71 GLN 71 184 184 GLN GLN A . n A 1 72 VAL 72 185 185 VAL VAL A . n A 1 73 ILE 73 186 186 ILE ILE A . n A 1 74 ASP 74 187 187 ASP ASP A . n A 1 75 LEU 75 188 188 LEU LEU A . n A 1 76 GLN 76 189 189 GLN GLN A . n A 1 77 ALA 77 190 190 ALA ALA A . n A 1 78 GLU 78 191 191 GLU GLU A . n A 1 79 GLY 79 192 192 GLY GLY A . n A 1 80 TYR 80 193 193 TYR TYR A . n A 1 81 TRP 81 194 194 TRP TRP A . n A 1 82 GLU 82 195 195 GLU GLU A . n A 1 83 GLU 83 196 196 GLU GLU A . n A 1 84 LEU 84 197 197 LEU LEU A . n A 1 85 LEU 85 198 198 LEU LEU A . n A 1 86 ASP 86 199 199 ASP ASP A . n A 1 87 THR 87 200 200 THR THR A . n A 1 88 THR 88 201 201 THR THR A . n A 1 89 GLN 89 202 202 GLN GLN A . n A 1 90 PRO 90 203 203 PRO PRO A . n A 1 91 ALA 91 204 204 ALA ALA A . n A 1 92 ILE 92 205 205 ILE ILE A . n A 1 93 VAL 93 206 206 VAL VAL A . n A 1 94 VAL 94 207 207 VAL VAL A . n A 1 95 LYS 95 208 208 LYS LYS A . n A 1 96 ASP 96 209 209 ASP ASP A . n A 1 97 TRP 97 210 210 TRP TRP A . n A 1 98 TYR 98 211 211 TYR TYR A . n A 1 99 SER 99 212 212 SER SER A . n A 1 100 GLY 100 213 213 GLY GLY A . n A 1 101 ARG 101 214 214 ARG ARG A . n A 1 102 THR 102 215 215 THR THR A . n A 1 103 ASP 103 216 216 ASP ASP A . n A 1 104 ALA 104 217 217 ALA ALA A . n A 1 105 GLY 105 218 218 GLY GLY A . n A 1 106 SER 106 219 219 SER SER A . n A 1 107 LEU 107 220 220 LEU LEU A . n A 1 108 TYR 108 221 221 TYR TYR A . n A 1 109 GLU 109 222 222 GLU GLU A . n A 1 110 LEU 110 223 223 LEU LEU A . n A 1 111 THR 111 224 224 THR THR A . n A 1 112 VAL 112 225 225 VAL VAL A . n A 1 113 ARG 113 226 226 ARG ARG A . n A 1 114 LEU 114 227 227 LEU LEU A . n A 1 115 LEU 115 228 228 LEU LEU A . n A 1 116 SER 116 229 229 SER SER A . n A 1 117 GLU 117 230 230 GLU GLU A . n A 1 118 ASN 118 231 231 ASN ASN A . n A 1 119 GLU 119 232 232 GLU GLU A . n A 1 120 ASP 120 233 233 ASP ASP A . n A 1 121 VAL 121 234 234 VAL VAL A . n A 1 122 LEU 122 235 235 LEU LEU A . n A 1 123 ALA 123 236 236 ALA ALA A . n A 1 124 GLU 124 237 237 GLU GLU A . n A 1 125 PHE 125 238 238 PHE PHE A . n A 1 126 ALA 126 239 239 ALA ALA A . n A 1 127 THR 127 240 240 THR THR A . n A 1 128 GLY 128 241 241 GLY GLY A . n A 1 129 GLN 129 242 242 GLN GLN A . n A 1 130 VAL 130 243 243 VAL VAL A . n A 1 131 ALA 131 244 244 ALA ALA A . n A 1 132 VAL 132 245 245 VAL VAL A . n A 1 133 PRO 133 246 246 PRO PRO A . n A 1 134 GLU 134 247 247 GLU GLU A . n A 1 135 ASP 135 248 248 ASP ASP A . n A 1 136 GLY 136 249 249 GLY GLY A . n A 1 137 SER 137 250 250 SER SER A . n A 1 138 TRP 138 251 251 TRP TRP A . n A 1 139 MET 139 252 252 MET MET A . n A 1 140 GLU 140 253 253 GLU GLU A . n A 1 141 ILE 141 254 254 ILE ILE A . n A 1 142 SER 142 255 255 SER SER A . n A 1 143 HIS 143 256 256 HIS HIS A . n A 1 144 THR 144 257 257 THR THR A . n A 1 145 PHE 145 258 258 PHE PHE A . n A 1 146 ILE 146 259 259 ILE ILE A . n A 1 147 ASP 147 260 260 ASP ASP A . n A 1 148 TYR 148 261 261 TYR TYR A . n A 1 149 GLY 149 262 262 GLY GLY A . n A 1 150 PRO 150 263 263 PRO PRO A . n A 1 151 GLY 151 264 264 GLY GLY A . n A 1 152 VAL 152 265 265 VAL VAL A . n A 1 153 ARG 153 266 266 ARG ARG A . n A 1 154 PHE 154 267 267 PHE PHE A . n A 1 155 VAL 155 268 268 VAL VAL A . n A 1 156 ARG 156 269 269 ARG ARG A . n A 1 157 PHE 157 270 270 PHE PHE A . n A 1 158 GLU 158 271 271 GLU GLU A . n A 1 159 HIS 159 272 272 HIS HIS A . n A 1 160 GLY 160 273 273 GLY GLY A . n A 1 161 GLY 161 274 274 GLY GLY A . n A 1 162 GLN 162 275 275 GLN GLN A . n A 1 163 ASP 163 276 276 ASP ASP A . n A 1 164 SER 164 277 277 SER SER A . n A 1 165 VAL 165 278 278 VAL VAL A . n A 1 166 TYR 166 279 279 TYR TYR A . n A 1 167 TRP 167 280 280 TRP TRP A . n A 1 168 LYS 168 281 281 LYS LYS A . n A 1 169 GLY 169 282 282 GLY GLY A . n A 1 170 TRP 170 283 283 TRP TRP A . n A 1 171 PHE 171 284 284 PHE PHE A . n A 1 172 GLY 172 285 285 GLY GLY A . n A 1 173 ALA 173 286 286 ALA ALA A . n A 1 174 ARG 174 287 287 ARG ARG A . n A 1 175 VAL 175 288 288 VAL VAL A . n A 1 176 THR 176 289 289 THR THR A . n A 1 177 ASN 177 290 290 ASN ASN A . n A 1 178 SER 178 291 291 SER SER A . n A 1 179 SER 179 292 292 SER SER A . n A 1 180 VAL 180 293 293 VAL VAL A . n A 1 181 TRP 181 294 294 TRP TRP A . n A 1 182 VAL 182 295 295 VAL VAL A . n A 1 183 GLU 183 296 296 GLU GLU A . n A 1 184 PRO 184 297 297 PRO PRO A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # 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 NI 1 501 1 NI NI A . C 3 HOH 1 1 1 HOH HOH A . C 3 HOH 2 2 2 HOH HOH A . C 3 HOH 3 3 3 HOH HOH A . C 3 HOH 4 4 4 HOH HOH A . C 3 HOH 5 5 5 HOH HOH A . C 3 HOH 6 6 6 HOH HOH A . C 3 HOH 7 7 7 HOH HOH A . C 3 HOH 8 8 8 HOH HOH A . C 3 HOH 9 9 9 HOH HOH A . C 3 HOH 10 10 10 HOH HOH A . C 3 HOH 11 11 11 HOH HOH A . C 3 HOH 12 12 12 HOH HOH A . C 3 HOH 13 13 13 HOH HOH A . C 3 HOH 14 14 14 HOH HOH A . C 3 HOH 15 15 15 HOH HOH A . C 3 HOH 16 16 16 HOH HOH A . C 3 HOH 17 17 17 HOH HOH A . C 3 HOH 18 18 18 HOH HOH A . C 3 HOH 19 19 19 HOH HOH A . C 3 HOH 20 20 20 HOH HOH A . C 3 HOH 21 21 21 HOH HOH A . C 3 HOH 22 22 22 HOH HOH A . C 3 HOH 23 23 23 HOH HOH A . C 3 HOH 24 24 24 HOH HOH A . C 3 HOH 25 25 25 HOH HOH A . C 3 HOH 26 26 26 HOH HOH A . C 3 HOH 27 27 27 HOH HOH A . C 3 HOH 28 28 28 HOH HOH A . C 3 HOH 29 29 29 HOH HOH A . C 3 HOH 30 30 30 HOH HOH A . C 3 HOH 31 31 31 HOH HOH A . C 3 HOH 32 32 32 HOH HOH A . C 3 HOH 33 33 33 HOH HOH A . C 3 HOH 34 34 34 HOH HOH A . C 3 HOH 35 35 35 HOH HOH A . C 3 HOH 36 36 36 HOH HOH A . C 3 HOH 37 37 37 HOH HOH A . C 3 HOH 38 38 38 HOH HOH A . C 3 HOH 39 39 39 HOH HOH A . C 3 HOH 40 40 40 HOH HOH A . C 3 HOH 41 41 41 HOH HOH A . C 3 HOH 42 42 42 HOH HOH A . C 3 HOH 43 43 43 HOH HOH A . C 3 HOH 44 44 44 HOH HOH A . C 3 HOH 45 45 45 HOH HOH A . C 3 HOH 46 46 46 HOH HOH A . C 3 HOH 47 47 47 HOH HOH A . C 3 HOH 48 48 48 HOH HOH A . C 3 HOH 49 49 49 HOH HOH A . C 3 HOH 50 50 50 HOH HOH A . C 3 HOH 51 51 51 HOH HOH A . C 3 HOH 52 52 52 HOH HOH A . C 3 HOH 53 53 53 HOH HOH A . C 3 HOH 54 54 54 HOH HOH A . C 3 HOH 55 55 55 HOH HOH A . C 3 HOH 56 56 56 HOH HOH A . C 3 HOH 57 57 57 HOH HOH A . C 3 HOH 58 58 58 HOH HOH A . C 3 HOH 59 59 59 HOH HOH A . C 3 HOH 60 60 60 HOH HOH A . C 3 HOH 61 61 61 HOH HOH A . C 3 HOH 62 62 62 HOH HOH A . C 3 HOH 63 63 63 HOH HOH A . C 3 HOH 64 64 64 HOH HOH A . C 3 HOH 65 65 65 HOH HOH A . C 3 HOH 66 66 66 HOH HOH A . C 3 HOH 67 67 67 HOH HOH A . C 3 HOH 68 68 68 HOH HOH A . C 3 HOH 69 69 69 HOH HOH A . C 3 HOH 70 70 70 HOH HOH A . C 3 HOH 71 71 71 HOH HOH A . C 3 HOH 72 72 72 HOH HOH A . C 3 HOH 73 73 73 HOH HOH A . C 3 HOH 74 74 74 HOH HOH A . C 3 HOH 75 75 75 HOH HOH A . C 3 HOH 76 76 76 HOH HOH A . C 3 HOH 77 77 77 HOH HOH A . C 3 HOH 78 78 78 HOH HOH A . C 3 HOH 79 79 79 HOH HOH A . C 3 HOH 80 80 80 HOH HOH A . C 3 HOH 81 81 81 HOH HOH A . C 3 HOH 82 82 82 HOH HOH A . C 3 HOH 83 83 83 HOH HOH A . C 3 HOH 84 84 84 HOH HOH A . C 3 HOH 85 85 85 HOH HOH A . C 3 HOH 86 86 86 HOH HOH A . C 3 HOH 87 87 87 HOH HOH A . C 3 HOH 88 88 88 HOH HOH A . C 3 HOH 89 89 89 HOH HOH A . C 3 HOH 90 90 90 HOH HOH A . C 3 HOH 91 91 91 HOH HOH A . C 3 HOH 92 92 92 HOH HOH A . C 3 HOH 93 93 93 HOH HOH A . C 3 HOH 94 94 94 HOH HOH A . C 3 HOH 95 95 95 HOH HOH A . C 3 HOH 96 96 96 HOH HOH A . C 3 HOH 97 97 97 HOH HOH A . C 3 HOH 98 98 98 HOH HOH A . C 3 HOH 99 99 99 HOH HOH A . C 3 HOH 100 100 100 HOH HOH A . C 3 HOH 101 101 101 HOH HOH A . C 3 HOH 102 102 102 HOH HOH A . C 3 HOH 103 103 103 HOH HOH A . C 3 HOH 104 104 104 HOH HOH A . C 3 HOH 105 105 105 HOH HOH A . C 3 HOH 106 106 106 HOH HOH A . C 3 HOH 107 107 107 HOH HOH A . C 3 HOH 108 108 108 HOH HOH A . C 3 HOH 109 109 109 HOH HOH A . C 3 HOH 110 110 110 HOH HOH A . C 3 HOH 111 111 111 HOH HOH A . C 3 HOH 112 112 112 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N ? A GLY 1 ? A GLY 114 ? 1_555 NI ? B NI . ? A NI 501 ? 1_555 OG ? A SER 2 ? A SER 115 ? 1_555 167.2 ? 2 N ? A GLY 1 ? A GLY 114 ? 1_555 NI ? B NI . ? A NI 501 ? 1_555 N ? A SER 2 ? A SER 115 ? 1_555 108.2 ? 3 OG ? A SER 2 ? A SER 115 ? 1_555 NI ? B NI . ? A NI 501 ? 1_555 N ? A SER 2 ? A SER 115 ? 1_555 84.5 ? # 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 2004-04-06 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 # _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' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 MOSFLM 'data reduction' . ? 2 CCP4 'data scaling' '(SCALA)' ? 3 MLPHARE phasing . ? 4 # 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 OE1 A GLU 222 ? ? O A HOH 85 ? ? 2.05 2 1 OE1 A GLU 178 ? ? O A HOH 82 ? ? 2.13 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 CA A SER 115 ? ? CB A SER 115 ? ? 1.626 1.525 0.101 0.015 N 2 1 CB A SER 115 ? ? OG A SER 115 ? ? 1.525 1.418 0.107 0.013 N # 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 GLY 114 ? ? CA A GLY 114 ? ? C A GLY 114 ? ? 128.62 113.10 15.52 2.50 N 2 1 NE A ARG 123 ? ? CZ A ARG 123 ? ? NH1 A ARG 123 ? ? 123.70 120.30 3.40 0.50 N 3 1 NE A ARG 123 ? ? CZ A ARG 123 ? ? NH2 A ARG 123 ? ? 116.42 120.30 -3.88 0.50 N 4 1 NE A ARG 124 ? ? CZ A ARG 124 ? ? NH1 A ARG 124 ? ? 124.49 120.30 4.19 0.50 N 5 1 NE A ARG 124 ? ? CZ A ARG 124 ? ? NH2 A ARG 124 ? ? 117.01 120.30 -3.29 0.50 N 6 1 CB A ASP 148 ? ? CG A ASP 148 ? ? OD2 A ASP 148 ? ? 124.83 118.30 6.53 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 ASP A 136 ? ? 57.67 -126.32 2 1 GLN A 165 ? ? 169.47 -35.70 3 1 ASP A 166 ? ? -133.17 -33.46 4 1 ASP A 167 ? ? 68.73 -30.88 5 1 SER A 176 ? ? -122.58 -149.96 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NICKEL (II) ION' NI 3 water HOH #