data_2FXY # _entry.id 2FXY # _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 2FXY pdb_00002fxy 10.2210/pdb2fxy/pdb RCSB RCSB036442 ? ? WWPDB D_1000036442 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2FXZ _pdbx_database_related.details 'a different fragment from the same protein' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2FXY _pdbx_database_status.recvd_initial_deposition_date 2006-02-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 'Wang, M.' 1 'Shan, L.' 2 'Wang, J.F.' 3 # _citation.id primary _citation.title ;Two peptide fragments G55-I72 and K97-A109 from staphylococcal nuclease exhibit different behaviors in conformational preferences for helix formation ; _citation.journal_abbrev Biopolymers _citation.journal_volume 83 _citation.page_first 268 _citation.page_last 279 _citation.year 2006 _citation.journal_id_ASTM BIPMAA _citation.country US _citation.journal_id_ISSN 0006-3525 _citation.journal_id_CSD 0161 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16767771 _citation.pdbx_database_id_DOI 10.1002/bip.20558 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, M.' 1 ? primary 'Shan, L.' 2 ? primary 'Wang, J.F.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description '18-mer peptide from Thermonuclease' _entity.formula_weight 1953.305 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec 3.1.31.1 _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name SNase # _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 GPEASAFTKKMVENAKKI _entity_poly.pdbx_seq_one_letter_code_can GPEASAFTKKMVENAKKI _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 PRO n 1 3 GLU n 1 4 ALA n 1 5 SER n 1 6 ALA n 1 7 PHE n 1 8 THR n 1 9 LYS n 1 10 LYS n 1 11 MET n 1 12 VAL n 1 13 GLU n 1 14 ASN n 1 15 ALA n 1 16 LYS n 1 17 LYS n 1 18 ILE 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 'The peptide was chemically synthesized. The sequence of the peptide is naturally found in Staphylococcus aureus.' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NUC_STAAU _struct_ref.pdbx_db_accession P00644 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GPEASAFTKKMVENAKKI _struct_ref.pdbx_align_begin 137 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2FXY _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 18 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P00644 _struct_ref_seq.db_align_beg 137 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 154 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 55 _struct_ref_seq.pdbx_auth_seq_align_end 72 # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 ILE 'L-peptide linking' y ISOLEUCINE ? '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 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 DQF-COSY, 2D TOCSY, 2D ROESY' 1 2 1 '2D_13C HSQC, 2D_13C HSQC-TOCSY' 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 5.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '2.0mM peptides; DSS, NaN3; 40% trifluoroethanol-d4, 60% H2O' '40% trifluoroethanol-d4, 60% H2O' 2 '2.0mM peptides; DSS, NaN3; 40% trifluoroethanol-d4, 60% D2O' '40% trifluoroethanol-d4, 60% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2FXY _pdbx_nmr_refine.method 'torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2FXY _pdbx_nmr_ensemble.conformers_calculated_total_number 80 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _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 2FXY _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal collection XwinNMR 3.5 Bruker 1 'data analysis' Felix 98 'MSI/Accelrys Inc.' 2 'structure solution' CNS 1.1 Brunger 3 refinement CNS 1.1 Brunger 4 # _exptl.entry_id 2FXY _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2FXY _struct.title 'Solution structure of 55-72 segment of staphylococcal nuclease' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2FXY _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'SNase(55-72), solution structure, HYDROLASE' # _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_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLU _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 3 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ALA _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 15 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLU _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 57 _struct_conf.end_auth_comp_id ALA _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 69 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _database_PDB_matrix.entry_id 2FXY _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 2FXY _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 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 55 55 GLY GLY A . n A 1 2 PRO 2 56 56 PRO PRO A . n A 1 3 GLU 3 57 57 GLU GLU A . n A 1 4 ALA 4 58 58 ALA ALA A . n A 1 5 SER 5 59 59 SER SER A . n A 1 6 ALA 6 60 60 ALA ALA A . n A 1 7 PHE 7 61 61 PHE PHE A . n A 1 8 THR 8 62 62 THR THR A . n A 1 9 LYS 9 63 63 LYS LYS A . n A 1 10 LYS 10 64 64 LYS LYS A . n A 1 11 MET 11 65 65 MET MET A . n A 1 12 VAL 12 66 66 VAL VAL A . n A 1 13 GLU 13 67 67 GLU GLU A . n A 1 14 ASN 14 68 68 ASN ASN A . n A 1 15 ALA 15 69 69 ALA ALA A . n A 1 16 LYS 16 70 70 LYS LYS A . n A 1 17 LYS 17 71 71 LYS LYS A . n A 1 18 ILE 18 72 72 ILE ILE 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 2006-12-19 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 PRO A 56 ? ? -91.11 -60.41 2 1 ALA A 69 ? ? -146.31 37.06 3 2 PRO A 56 ? ? -91.06 -60.31 4 3 PRO A 56 ? ? -91.12 -60.34 5 3 ALA A 58 ? ? -137.46 -64.72 6 3 ALA A 69 ? ? -146.34 36.90 7 4 PRO A 56 ? ? -91.13 -60.41 8 4 ALA A 69 ? ? -153.10 39.48 9 5 PRO A 56 ? ? -91.08 -60.38 10 5 ALA A 69 ? ? -149.42 38.27 11 6 PRO A 56 ? ? -91.13 -60.37 12 6 ALA A 58 ? ? -97.69 -72.29 13 7 PRO A 56 ? ? -91.08 -60.38 14 7 ALA A 58 ? ? -107.49 -69.25 15 7 ALA A 69 ? ? -153.25 39.57 16 8 PRO A 56 ? ? -91.15 -60.33 17 9 PRO A 56 ? ? -91.07 -60.37 18 9 ALA A 69 ? ? -144.64 35.03 19 9 LYS A 71 ? ? 70.61 34.26 20 10 PRO A 56 ? ? -91.11 -60.36 21 10 ALA A 58 ? ? -104.97 -73.76 22 10 ALA A 69 ? ? -149.07 38.11 23 11 PRO A 56 ? ? -91.13 -60.40 24 11 ALA A 58 ? ? -131.20 -53.32 25 11 ALA A 69 ? ? -146.28 36.96 26 12 PRO A 56 ? ? -91.09 -60.35 27 12 ALA A 69 ? ? -153.06 39.49 28 13 PRO A 56 ? ? -91.04 -60.38 29 14 PRO A 56 ? ? -91.13 -60.31 30 14 ALA A 69 ? ? -149.42 38.24 31 15 PRO A 56 ? ? -91.08 -60.33 32 15 ALA A 58 ? ? -97.82 -67.12 #