data_2BBL # _entry.id 2BBL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2BBL pdb_00002bbl 10.2210/pdb2bbl/pdb RCSB RCSB034910 ? ? WWPDB D_1000034910 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2BBP _pdbx_database_related.details 'NMR structures of the peptide linked to the genome (VPg) of poliovirus' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2BBL _pdbx_database_status.recvd_initial_deposition_date 2005-10-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Schein, C.H.' 1 'Oezguen, N.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.' Peptides 27 1676 1684 2006 ? US 0196-9781 ? ? 16540201 10.1016/j.peptides.2006.01.018 1 'Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses' Proteins ? ? ? 2006 PSFGEY US 1097-0134 0867 ? 16498624 10.1002/prot.20891 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schein, C.H.' 1 ? primary 'Oezguen, N.' 2 ? primary 'Volk, D.E.' 3 ? primary 'Garimella, R.' 4 ? primary 'Paul, A.' 5 ? primary 'Braun, W.' 6 ? 1 'Schein, C.H.' 7 ? 1 'Volk, D.E.' 8 ? 1 'Oezguen, N.' 9 ? 1 'Paul, A.' 10 ? # _cell.entry_id 2BBL _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BBL _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Genome linked protein VPg' _entity.formula_weight 2357.749 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'residues 1-22' _entity.details ? # _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 GAYTGLPNKKPNVPTIRTAKVQ _entity_poly.pdbx_seq_one_letter_code_can GAYTGLPNKKPNVPTIRTAKVQ _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ALA n 1 3 TYR n 1 4 THR n 1 5 GLY n 1 6 LEU n 1 7 PRO n 1 8 ASN n 1 9 LYS n 1 10 LYS n 1 11 PRO n 1 12 ASN n 1 13 VAL n 1 14 PRO n 1 15 THR n 1 16 ILE n 1 17 ARG n 1 18 THR n 1 19 ALA n 1 20 LYS n 1 21 VAL n 1 22 GLN n # _pdbx_entity_src_syn.entity_id 1 _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 'This sequence occurs naturally in human poliovirus serotype 1.' # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code NP_740475 _struct_ref.pdbx_db_accession 25121847 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GAYTGLPNKKPNVPTIRTAKVQ _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2BBL _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 22 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 25121847 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 22 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 22 # 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 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.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D TOCSY' 1 2 1 '2D NOESY' 1 3 1 DQF-COSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 283 _pdbx_nmr_exptl_sample_conditions.pressure atmospheric _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.ionic_strength '10mM sodium phosphate' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'VPg 2.78 mM, 0.01 M sodium phosphate buffer, pH 7.2, 4M deuterated Trimethylamine oxide, 10% D2O' _pdbx_nmr_sample_details.solvent_system 10%D2O # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 UNITYPLUS Varian 750 ? 2 UNITYPLUS Varian 600 ? # _pdbx_nmr_refine.entry_id 2BBL _pdbx_nmr_refine.method 'automatic NOE assignment in combination with distance geometry' _pdbx_nmr_refine.details ;Refinement of the NOE assignment is performed iteratively. NOAH passes geometrical constraints derived from the NOE list to DIAMOD. DIAMOD calculates a bundle of structures with least violation of the constraints. The new bundle of structures is the basis for refinement of the assignments in NOAH. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2BBL _pdbx_nmr_details.text 'Spectra were collected at 283K' # _pdbx_nmr_ensemble.entry_id 2BBL _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 2BBL _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' NOAH 2.0 'Mumenthaler, C. et al' 1 'structure solution' DIAMOD 2.2 'Guentert, P. et al' 2 'data analysis' Felix ? ? 3 refinement DIAMOD 2.2 'Guentert, P. et al' 4 # _exptl.entry_id 2BBL _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 2BBL _struct.title 'NMR structures of the peptide linked to the genome (VPg) of poliovirus in a stabilizing solvent' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2BBL _struct_keywords.pdbx_keywords 'VIRAL PROTEIN' _struct_keywords.text 'peptide primer, RNA synthesis, uridylylation, viral replication, polymerase cofactor, VIRAL PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id ILE _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 16 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLN _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 22 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ILE _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 16 _struct_conf.end_auth_comp_id GLN _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 22 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2BBL _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 2BBL _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 # 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 1 1 GLY GLY A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 TYR 3 3 3 TYR TYR A . n A 1 4 THR 4 4 4 THR THR A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 PRO 7 7 7 PRO PRO A . n A 1 8 ASN 8 8 8 ASN ASN A . n A 1 9 LYS 9 9 9 LYS LYS A . n A 1 10 LYS 10 10 10 LYS LYS A . n A 1 11 PRO 11 11 11 PRO PRO A . n A 1 12 ASN 12 12 12 ASN ASN A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 PRO 14 14 14 PRO PRO A . n A 1 15 THR 15 15 15 THR THR A . n A 1 16 ILE 16 16 16 ILE ILE A . n A 1 17 ARG 17 17 17 ARG ARG A . n A 1 18 THR 18 18 18 THR THR A . n A 1 19 ALA 19 19 19 ALA ALA A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 GLN 22 22 22 GLN GLN A . n # _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 # _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 2006-03-28 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # 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 A 8 ? ? 64.73 102.68 2 1 LYS A 9 ? ? -131.86 -83.76 3 1 LYS A 10 ? ? -178.97 -63.97 4 1 ASN A 12 ? ? -166.48 83.34 5 2 ALA A 2 ? ? 61.58 172.67 6 2 THR A 4 ? ? -149.02 -49.31 7 2 ASN A 8 ? ? 57.32 75.69 8 2 LYS A 9 ? ? -114.24 -81.98 9 2 LYS A 10 ? ? -179.38 -62.94 10 2 ASN A 12 ? ? -163.50 90.59 11 3 ALA A 2 ? ? 58.52 171.40 12 3 ASN A 8 ? ? 61.48 103.20 13 3 LYS A 9 ? ? -130.12 -88.14 14 3 LYS A 10 ? ? -178.61 -66.08 15 3 ASN A 12 ? ? -172.06 96.25 16 4 ALA A 2 ? ? 61.60 172.78 17 4 THR A 4 ? ? -147.90 -49.06 18 4 ASN A 8 ? ? 61.41 77.16 19 4 LYS A 9 ? ? -115.28 -82.43 20 4 LYS A 10 ? ? -179.46 -63.17 21 4 ASN A 12 ? ? -164.56 90.08 22 5 ALA A 2 ? ? 59.67 171.51 23 5 ASN A 8 ? ? 64.03 103.68 24 5 LYS A 9 ? ? -131.76 -89.92 25 5 LYS A 10 ? ? -179.08 -66.63 26 5 ASN A 12 ? ? -172.29 96.90 27 6 ASN A 8 ? ? 64.51 103.74 28 6 LYS A 9 ? ? -131.08 -87.84 29 6 LYS A 10 ? ? -178.88 -65.49 30 6 ASN A 12 ? ? -170.04 93.86 31 7 ASN A 8 ? ? 63.78 115.19 32 7 LYS A 9 ? ? -134.39 -88.33 33 7 LYS A 10 ? ? -178.06 -60.71 34 7 ASN A 12 ? ? -140.17 55.81 35 8 ASN A 8 ? ? 63.37 102.24 36 8 LYS A 9 ? ? -130.61 -87.18 37 8 LYS A 10 ? ? -178.53 -65.48 38 8 ASN A 12 ? ? -170.09 91.82 39 9 ASN A 8 ? ? 37.45 90.48 40 9 LYS A 9 ? ? -116.29 -84.13 41 9 LYS A 10 ? ? -177.94 -64.29 42 9 ASN A 12 ? ? -169.17 84.09 43 10 ASN A 8 ? ? 60.42 91.40 44 10 LYS A 9 ? ? -117.70 -89.44 45 10 LYS A 10 ? ? 179.12 -64.99 46 10 ASN A 12 ? ? -171.30 90.91 #