data_2M7D # _entry.id 2M7D # _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 2M7D RCSB RCSB103301 BMRB 19183 WWPDB D_1000103301 # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2m7c PDB 'circular permutation of the Trp-cage' unspecified 2jof PDB 'partly optimized Trp-cage' unspecified 1l2y PDB 'original, non-optimized Trp-cage' unspecified 1rij PDB 'Trp-cage with modified salt-bridge' unspecified 2ldj PDB 'Trp-cage containing D-amino acid' unspecified 2ll5 PDB 'cyclic Trp-cage' unspecified 19183 BMRB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2M7D _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-04-19 _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Williams, D.V.' 1 'Andersen, N.H.' 2 'Kier, B.L.' 3 # _citation.id primary _citation.title 'Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple.' _citation.journal_abbrev 'RSC Adv' _citation.journal_volume 2013 _citation.page_first 19824 _citation.page_last 19829 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2046-2069 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24376912 _citation.pdbx_database_id_DOI 10.1039/C3RA43674H # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Byrne, A.' 1 primary 'Kier, B.L.' 2 primary 'Williams, D.V.' 3 primary 'Scian, M.' 4 primary 'Andersen, N.H.' 5 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Trp-Cage mini-protein' _entity.formula_weight 2131.283 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation 'P12W, G10a, G15a' _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'DAYAQWLAD(DAL)GWAS(DAL)RPPPS' _entity_poly.pdbx_seq_one_letter_code_can DAYAQWLADAGWASARPPPS _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 ASP n 1 2 ALA n 1 3 TYR n 1 4 ALA n 1 5 GLN n 1 6 TRP n 1 7 LEU n 1 8 ALA n 1 9 ASP n 1 10 DAL n 1 11 GLY n 1 12 TRP n 1 13 ALA n 1 14 SER n 1 15 DAL n 1 16 ARG n 1 17 PRO n 1 18 PRO n 1 19 PRO n 1 20 SER n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2M7D _struct_ref.pdbx_db_accession 2M7D _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code DAYAQWLADAGWASARPPPS _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2M7D _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 20 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2M7D _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 20 _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 20 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 DAL 'D-peptide linking' . D-ALANINE ? 'C3 H7 N O2' 89.093 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.type '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.11 _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 280 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '50 mM sodium phosphate, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker DMX' # _pdbx_nmr_refine.entry_id 2M7D _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'Incorporated LJ potential relax as extra final step for improved refinement.' _pdbx_nmr_refine.software_ordinal 1 # _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 lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 30 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2M7D _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 2M7D _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger, Adams, Clore, Gros, Nilges and Read' 'structure solution' CNS 1.2 1 ? refinement CNS ? 2 # _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 ? _exptl.entry_id 2M7D _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2M7D _struct.title 'Trp-cage 16b P12W: a Hyperstable Miniprotein' _struct.pdbx_descriptor 'Trp-Cage mini-protein' _struct.pdbx_model_details 'closest to the average, model1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2M7D _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' _struct_keywords.text 'miniprotein, de novo protein, Trp-cage, circular permutant, microprotein' # _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 ALA _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 2 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ASP _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 9 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ALA _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 2 _struct_conf.end_auth_comp_id ASP _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 9 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 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 covale1 covale ? ? A ASP 9 C ? ? ? 1_555 A DAL 10 N ? ? A ASP 9 A DAL 10 1_555 ? ? ? ? ? ? ? 1.337 ? covale2 covale ? ? A DAL 10 C ? ? ? 1_555 A GLY 11 N ? ? A DAL 10 A GLY 11 1_555 ? ? ? ? ? ? ? 1.338 ? covale3 covale ? ? A SER 14 C ? ? ? 1_555 A DAL 15 N ? ? A SER 14 A DAL 15 1_555 ? ? ? ? ? ? ? 1.338 ? covale4 covale ? ? A DAL 15 C ? ? ? 1_555 A ARG 16 N ? ? A DAL 15 A ARG 16 1_555 ? ? ? ? ? ? ? 1.331 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _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 _struct_site.details AC1 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE DAL A 10' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE DAL A 15' # 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 6 LEU A 7 ? LEU A 7 . ? 1_555 ? 2 AC1 6 ALA A 8 ? ALA A 8 . ? 1_555 ? 3 AC1 6 ASP A 9 ? ASP A 9 . ? 1_555 ? 4 AC1 6 GLY A 11 ? GLY A 11 . ? 1_555 ? 5 AC1 6 TRP A 12 ? TRP A 12 . ? 1_555 ? 6 AC1 6 ALA A 13 ? ALA A 13 . ? 1_555 ? 7 AC2 4 TRP A 12 ? TRP A 12 . ? 1_555 ? 8 AC2 4 ALA A 13 ? ALA A 13 . ? 1_555 ? 9 AC2 4 SER A 14 ? SER A 14 . ? 1_555 ? 10 AC2 4 ARG A 16 ? ARG A 16 . ? 1_555 ? # _atom_sites.entry_id 2M7D _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 ASP 1 1 1 ASP ASP 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 ALA 4 4 4 ALA ALA A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 TRP 6 6 6 TRP TRP A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 ASP 9 9 9 ASP ASP A . n A 1 10 DAL 10 10 10 DAL DAL A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 TRP 12 12 12 TRP TRP A . n A 1 13 ALA 13 13 13 ALA ALA A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 DAL 15 15 15 DAL DAL A . n A 1 16 ARG 16 16 16 ARG ARG A . n A 1 17 PRO 17 17 17 PRO PRO A . n A 1 18 PRO 18 18 18 PRO PRO A . n A 1 19 PRO 19 19 19 PRO PRO A . n A 1 20 SER 20 20 20 SER SER 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 2013-12-25 2 'Structure model' 1 1 2014-01-15 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_nmr_exptl_sample.component 'sodium phosphate-1' _pdbx_nmr_exptl_sample.concentration 50 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2M7D _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 323 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 ALA A 2 ? ? -137.81 -69.42 2 3 ALA A 2 ? ? -128.63 -53.71 3 4 ALA A 2 ? ? 70.82 -74.58 4 7 ALA A 2 ? ? 73.93 -69.87 5 8 ALA A 2 ? ? -141.93 -64.89 6 9 ALA A 2 ? ? -127.19 -64.81 7 11 ALA A 2 ? ? -120.10 -65.81 8 13 ALA A 2 ? ? -124.60 -62.49 9 14 ALA A 2 ? ? -122.94 -67.79 10 15 ALA A 2 ? ? -157.81 -67.93 11 18 ALA A 2 ? ? -152.68 -66.44 12 19 ALA A 2 ? ? -131.22 -68.80 13 21 ALA A 2 ? ? -148.66 -67.42 14 25 ALA A 2 ? ? 74.33 -72.76 15 29 ALA A 2 ? ? 67.78 -75.09 16 30 ALA A 2 ? ? 69.02 -75.87 #