data_2MRO # _entry.id 2MRO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2MRO pdb_00002mro 10.2210/pdb2mro/pdb RCSB RCSB103971 ? ? WWPDB D_1000103971 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 1d3z PDB 'UBIQUITIN NMR STRUCTURE' unspecified 2MR9 PDB 'UBA domain of DNA-damage-inducible 1 protein (Ddi1)' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2MRO _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-07-14 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhang, D.' 1 'Fushman, D.' 2 # _citation.id primary _citation.title 'DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.' _citation.journal_abbrev Structure _citation.journal_volume 23 _citation.page_first 542 _citation.page_last 557 _citation.year 2015 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25703377 _citation.pdbx_database_id_DOI 10.1016/j.str.2015.01.010 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nowicka, U.' 1 ? primary 'Zhang, D.' 2 ? primary 'Walker, O.' 3 ? primary 'Krutauz, D.' 4 ? primary 'Castaneda, C.A.' 5 ? primary 'Chaturvedi, A.' 6 ? primary 'Chen, T.Y.' 7 ? primary 'Reis, N.' 8 ? primary 'Glickman, M.H.' 9 ? primary 'Fushman, D.' 10 ? # 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 Polyubiquitin-B 8576.831 1 ? ? 'Human Ubiquitin' ? 2 polymer man 'DNA damage-inducible protein 1' 4745.367 1 ? ? 'Ubiquitin associated domain, UNP residues 389-428' ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 Ubiquitin 2 'v-SNARE-master 1' # 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 no MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG A ? 2 'polypeptide(L)' no no GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS GSATFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQS B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLN n 1 3 ILE n 1 4 PHE n 1 5 VAL n 1 6 LYS n 1 7 THR n 1 8 LEU n 1 9 THR n 1 10 GLY n 1 11 LYS n 1 12 THR n 1 13 ILE n 1 14 THR n 1 15 LEU n 1 16 GLU n 1 17 VAL n 1 18 GLU n 1 19 PRO n 1 20 SER n 1 21 ASP n 1 22 THR n 1 23 ILE n 1 24 GLU n 1 25 ASN n 1 26 VAL n 1 27 LYS n 1 28 ALA n 1 29 LYS n 1 30 ILE n 1 31 GLN n 1 32 ASP n 1 33 LYS n 1 34 GLU n 1 35 GLY n 1 36 ILE n 1 37 PRO n 1 38 PRO n 1 39 ASP n 1 40 GLN n 1 41 GLN n 1 42 ARG n 1 43 LEU n 1 44 ILE n 1 45 PHE n 1 46 ALA n 1 47 GLY n 1 48 LYS n 1 49 GLN n 1 50 LEU n 1 51 GLU n 1 52 ASP n 1 53 GLY n 1 54 ARG n 1 55 THR n 1 56 LEU n 1 57 SER n 1 58 ASP n 1 59 TYR n 1 60 ASN n 1 61 ILE n 1 62 GLN n 1 63 LYS n 1 64 GLU n 1 65 SER n 1 66 THR n 1 67 LEU n 1 68 HIS n 1 69 LEU n 1 70 VAL n 1 71 LEU n 1 72 ARG n 1 73 LEU n 1 74 ARG n 1 75 GLY n 1 76 GLY n 2 1 GLY n 2 2 SER n 2 3 ALA n 2 4 THR n 2 5 PHE n 2 6 PRO n 2 7 GLU n 2 8 GLN n 2 9 THR n 2 10 ILE n 2 11 LYS n 2 12 GLN n 2 13 LEU n 2 14 MET n 2 15 ASP n 2 16 LEU n 2 17 GLY n 2 18 PHE n 2 19 PRO n 2 20 ARG n 2 21 ASP n 2 22 ALA n 2 23 VAL n 2 24 VAL n 2 25 LYS n 2 26 ALA n 2 27 LEU n 2 28 LYS n 2 29 GLN n 2 30 THR n 2 31 ASN n 2 32 GLY n 2 33 ASN n 2 34 ALA n 2 35 GLU n 2 36 PHE n 2 37 ALA n 2 38 ALA n 2 39 SER n 2 40 LEU n 2 41 LEU n 2 42 PHE n 2 43 GLN n 2 44 SER n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _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 _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _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 _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _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 _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 _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? human ? UBB ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? 'BL21(DE3)pLysS' ? ? ? ? ? ? ? ? pET3a ? ? ? ? ? 2 1 sample ? ? ? ;Baker's yeast ; ? 'DDI1, VSM1, YER143W' ? 'ATCC 204508 / S288c' ? ? ? ? 'Saccharomyces cerevisiae' 559292 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? 'BL21(DE3)pLysS' ? ? ? ? ? ? ? ? 'pGEX 4T2' ? ? ? ? ? # 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 UBB_HUMAN P0CG47 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 1 ? 2 UNP DDI1_YEAST P40087 2 TFPEQTIKQLMDLGFPRDAVVKALKQTNGNAEFAASLLFQ 389 ? # 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 2MRO A 1 ? 76 ? P0CG47 1 ? 76 ? 1 76 2 2 2MRO B 4 ? 43 ? P40087 389 ? 428 ? 389 428 # 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 2 2MRO GLY B 1 ? UNP P40087 ? ? 'expression tag' 386 1 2 2MRO SER B 2 ? UNP P40087 ? ? 'expression tag' 387 2 2 2MRO ALA B 3 ? UNP P40087 ? ? 'expression tag' 388 3 2 2MRO SER B 44 ? UNP P40087 ? ? 'expression tag' 429 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 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-15N HSQC' 1 2 2 '2D 1H-15N HSQC' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 20 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298.2 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O' 1 '93% H2O/7% D2O' '1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O' 2 '93% H2O/7% D2O' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2MRO _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2MRO _pdbx_nmr_details.text 'Two titration experiments were conducted. Basically unlabeled ligand protein was added stepwise to N15-Labeled protein solution.' # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2MRO _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2MRO _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' collection TopSpin 2.1 1 'Bruker Biospin' processing TopSpin 2.1 2 'Keller and Wuthrich' 'chemical shift assignment' CARA 1.8.1 3 'Alexandre Bonvin' 'geometry optimization' HADDOCK 2.1 4 'Alexandre Bonvin' refinement HADDOCK 2.1 5 'Alexandre Bonvin' 'structure solution' HADDOCK 2.1 6 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details 'Complex structure based on chemical shift perturbation data and spin-labeling data, calculated using Haddock program' _exptl.entry_id 2MRO _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2MRO _struct.title 'Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)' _struct.pdbx_model_details 'lowest energy, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2MRO _struct_keywords.pdbx_keywords 'TRANSPORT PROTEIN/SIGNALING PROTEIN' _struct_keywords.text ;DNA-damage-inducible 1 protein, Ubiquitin associated domain, Ddi1, UBA, HYDROLASE-SIGNALING PROTEIN complex, TRANSPORT PROTEIN-SIGNALING PROTEIN complex ; # 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 ? # 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 THR A 22 ? GLY A 35 ? THR A 22 GLY A 35 1 ? 14 HELX_P HELX_P2 2 THR A 55 ? ASN A 60 ? THR A 55 ASN A 60 5 ? 6 HELX_P HELX_P3 3 PRO B 6 ? LEU B 16 ? PRO B 391 LEU B 401 1 ? 11 HELX_P HELX_P4 4 PRO B 19 ? GLN B 29 ? PRO B 404 GLN B 414 1 ? 11 HELX_P HELX_P5 5 ASN B 33 ? PHE B 42 ? ASN B 418 PHE B 427 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 THR A 12 ? GLU A 16 ? THR A 12 GLU A 16 A 2 GLN A 2 ? THR A 7 ? GLN A 2 THR A 7 A 3 THR A 66 ? LEU A 71 ? THR A 66 LEU A 71 A 4 GLN A 41 ? PHE A 45 ? GLN A 41 PHE A 45 A 5 LYS A 48 ? GLN A 49 ? LYS A 48 GLN A 49 # 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 ILE A 13 ? O ILE A 13 N VAL A 5 ? N VAL A 5 A 2 3 N PHE A 4 ? N PHE A 4 O LEU A 67 ? O LEU A 67 A 3 4 O VAL A 70 ? O VAL A 70 N ARG A 42 ? N ARG A 42 A 4 5 N PHE A 45 ? N PHE A 45 O LYS A 48 ? O LYS A 48 # _atom_sites.entry_id 2MRO _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 1.000000 _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] 1.000000 _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 H N O Q S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 GLN 2 2 2 GLN GLN A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 THR 9 9 9 THR THR A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 THR 12 12 12 THR THR A . n A 1 13 ILE 13 13 13 ILE ILE A . n A 1 14 THR 14 14 14 THR THR A . n A 1 15 LEU 15 15 15 LEU LEU A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 GLU 18 18 18 GLU GLU A . n A 1 19 PRO 19 19 19 PRO PRO A . n A 1 20 SER 20 20 20 SER SER A . n A 1 21 ASP 21 21 21 ASP ASP A . n A 1 22 THR 22 22 22 THR THR A . n A 1 23 ILE 23 23 23 ILE ILE A . n A 1 24 GLU 24 24 24 GLU GLU A . n A 1 25 ASN 25 25 25 ASN ASN A . n A 1 26 VAL 26 26 26 VAL VAL A . n A 1 27 LYS 27 27 27 LYS LYS A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 GLN 31 31 31 GLN GLN A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 LYS 33 33 33 LYS LYS A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 ILE 36 36 36 ILE ILE A . n A 1 37 PRO 37 37 37 PRO PRO A . n A 1 38 PRO 38 38 38 PRO PRO A . n A 1 39 ASP 39 39 39 ASP ASP A . n A 1 40 GLN 40 40 40 GLN GLN A . n A 1 41 GLN 41 41 41 GLN GLN A . n A 1 42 ARG 42 42 42 ARG ARG A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ILE 44 44 44 ILE ILE A . n A 1 45 PHE 45 45 45 PHE PHE A . n A 1 46 ALA 46 46 46 ALA ALA A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 LYS 48 48 48 LYS LYS A . n A 1 49 GLN 49 49 49 GLN GLN A . n A 1 50 LEU 50 50 50 LEU LEU A . n A 1 51 GLU 51 51 51 GLU GLU A . n A 1 52 ASP 52 52 52 ASP ASP A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 ARG 54 54 54 ARG ARG A . n A 1 55 THR 55 55 55 THR THR A . n A 1 56 LEU 56 56 56 LEU LEU A . n A 1 57 SER 57 57 57 SER SER A . n A 1 58 ASP 58 58 58 ASP ASP A . n A 1 59 TYR 59 59 59 TYR TYR A . n A 1 60 ASN 60 60 60 ASN ASN A . n A 1 61 ILE 61 61 61 ILE ILE A . n A 1 62 GLN 62 62 62 GLN GLN A . n A 1 63 LYS 63 63 63 LYS LYS A . n A 1 64 GLU 64 64 64 GLU GLU A . n A 1 65 SER 65 65 65 SER SER A . n A 1 66 THR 66 66 66 THR THR A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 HIS 68 68 68 HIS HIS A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 LEU 71 71 71 LEU LEU A . n A 1 72 ARG 72 72 72 ARG ARG A . n A 1 73 LEU 73 73 73 LEU LEU A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 GLY 75 75 75 GLY GLY A . n A 1 76 GLY 76 76 76 GLY GLY A . n B 2 1 GLY 1 386 386 GLY GLY B . n B 2 2 SER 2 387 387 SER SER B . n B 2 3 ALA 3 388 388 ALA ALA B . n B 2 4 THR 4 389 389 THR THR B . n B 2 5 PHE 5 390 390 PHE PHE B . n B 2 6 PRO 6 391 391 PRO PRO B . n B 2 7 GLU 7 392 392 GLU GLU B . n B 2 8 GLN 8 393 393 GLN GLN B . n B 2 9 THR 9 394 394 THR THR B . n B 2 10 ILE 10 395 395 ILE ILE B . n B 2 11 LYS 11 396 396 LYS LYS B . n B 2 12 GLN 12 397 397 GLN GLN B . n B 2 13 LEU 13 398 398 LEU LEU B . n B 2 14 MET 14 399 399 MET MET B . n B 2 15 ASP 15 400 400 ASP ASP B . n B 2 16 LEU 16 401 401 LEU LEU B . n B 2 17 GLY 17 402 402 GLY GLY B . n B 2 18 PHE 18 403 403 PHE PHE B . n B 2 19 PRO 19 404 404 PRO PRO B . n B 2 20 ARG 20 405 405 ARG ARG B . n B 2 21 ASP 21 406 406 ASP ASP B . n B 2 22 ALA 22 407 407 ALA ALA B . n B 2 23 VAL 23 408 408 VAL VAL B . n B 2 24 VAL 24 409 409 VAL VAL B . n B 2 25 LYS 25 410 410 LYS LYS B . n B 2 26 ALA 26 411 411 ALA ALA B . n B 2 27 LEU 27 412 412 LEU LEU B . n B 2 28 LYS 28 413 413 LYS LYS B . n B 2 29 GLN 29 414 414 GLN GLN B . n B 2 30 THR 30 415 415 THR THR B . n B 2 31 ASN 31 416 416 ASN ASN B . n B 2 32 GLY 32 417 417 GLY GLY B . n B 2 33 ASN 33 418 418 ASN ASN B . n B 2 34 ALA 34 419 419 ALA ALA B . n B 2 35 GLU 35 420 420 GLU GLU B . n B 2 36 PHE 36 421 421 PHE PHE B . n B 2 37 ALA 37 422 422 ALA ALA B . n B 2 38 ALA 38 423 423 ALA ALA B . n B 2 39 SER 39 424 424 SER SER B . n B 2 40 LEU 40 425 425 LEU LEU B . n B 2 41 LEU 41 426 426 LEU LEU B . n B 2 42 PHE 42 427 427 PHE PHE B . n B 2 43 GLN 43 428 428 GLN GLN B . n B 2 44 SER 44 429 429 SER SER B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # 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)' 1540 ? 1 MORE -6 ? 1 'SSA (A^2)' 7120 ? # _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 2015-02-04 2 'Structure model' 1 1 2015-03-18 3 'Structure model' 1 2 2019-11-06 4 'Structure model' 1 3 2023-06-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Experimental preparation' 5 4 'Structure model' 'Database references' 6 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_related 3 3 'Structure model' pdbx_nmr_sample_details 4 3 'Structure model' pdbx_nmr_software 5 3 'Structure model' pdbx_nmr_spectrometer 6 3 'Structure model' struct_ref_seq_dif 7 4 'Structure model' database_2 8 4 'Structure model' pdbx_database_status # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_pdbx_database_related.db_name' 2 3 'Structure model' '_pdbx_nmr_sample_details.contents' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_pdbx_nmr_spectrometer.model' 5 3 'Structure model' '_struct_ref_seq_dif.details' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' 8 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id Ub-1 1 ? mM '[U-100% 15N]' 1 'sodium phosphate-2' 20 ? mM ? 1 D2O-3 7 ? % '[U-99% 2H]' 1 H2O-4 93 ? % ? 1 UBA-5 1 ? mM '[U-100% 15N]' 2 'sodium phosphate-6' 20 ? mM ? 2 D2O-7 7 ? % '[U-99% 2H]' 2 H2O-8 93 ? % ? 2 # 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 HZ2 A LYS 6 ? ? OD2 B ASP 400 ? ? 1.57 2 1 OD2 A ASP 21 ? ? HZ2 A LYS 29 ? ? 1.57 3 2 OD1 B ASP 406 ? ? HZ3 B LYS 410 ? ? 1.56 4 2 HZ2 A LYS 11 ? ? OE2 A GLU 34 ? ? 1.58 5 2 HZ3 A LYS 27 ? ? OD1 A ASP 52 ? ? 1.59 6 2 HZ2 A LYS 6 ? ? OD2 B ASP 400 ? ? 1.59 7 5 OD2 A ASP 21 ? ? HZ1 A LYS 29 ? ? 1.54 8 6 H1 A MET 1 ? ? OE2 A GLU 16 ? ? 1.56 9 6 HZ2 A LYS 6 ? ? OD2 B ASP 400 ? ? 1.60 10 7 HZ2 A LYS 6 ? ? OD2 B ASP 400 ? ? 1.59 11 8 OD2 A ASP 21 ? ? HZ3 A LYS 29 ? ? 1.57 12 8 OD2 B ASP 406 ? ? HZ2 B LYS 410 ? ? 1.58 13 9 HZ1 A LYS 27 ? ? OD2 A ASP 52 ? ? 1.56 14 9 OD2 A ASP 21 ? ? HZ1 A LYS 29 ? ? 1.59 15 10 HZ2 A LYS 27 ? ? OD2 A ASP 52 ? ? 1.57 16 10 HZ3 A LYS 6 ? ? OD2 B ASP 400 ? ? 1.59 # 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 ASN B 416 ? ? 70.09 63.56 2 2 GLU A 34 ? ? -92.00 -65.27 3 2 GLN A 62 ? ? -106.33 -167.69 4 3 THR A 9 ? ? -79.26 29.84 5 3 GLN A 62 ? ? -114.94 -166.23 6 4 SER B 387 ? ? -143.00 39.88 7 4 ASN B 416 ? ? 68.30 62.10 8 5 GLN A 62 ? ? -106.14 -166.60 9 6 GLN A 62 ? ? -101.46 -167.06 10 6 ASN B 416 ? ? 61.82 60.85 11 7 ARG A 42 ? ? -160.37 94.51 12 7 GLN A 62 ? ? -109.50 -163.24 13 7 ARG A 74 ? ? -103.36 -63.25 14 7 ASN B 418 ? ? -67.80 93.99 15 8 GLN A 62 ? ? -107.92 -165.99 16 9 GLN A 62 ? ? -113.24 -164.35 17 9 ASN B 416 ? ? 61.96 61.10 18 10 GLN A 62 ? ? -110.96 -167.99 19 10 GLU A 64 ? ? 70.40 -1.53 #