data_2L77 # _entry.id 2L77 # _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 2L77 RCSB RCSB102043 WWPDB D_1000102043 # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.content_type 2L79 PDB 'Solution structure of PAP248-286 in 30% TFE' unspecified 17346 BMRB . unspecified # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2L77 _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2010-12-03 _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 ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nanga, R.' 1 'Brender, J.R.' 2 'Popovych, N.' 3 'Ramamoorthy, A.' 4 # _citation.id primary _citation.title 'Solution NMR structure of PAP248-286 in TFE' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Brender, J.R.' 1 primary 'Nanga, R.' 2 primary 'Popovych, N.' 3 primary 'Soong, R.' 4 primary 'MacDonald, P.M.' 5 primary 'Ramamoorthy, A.' 6 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Prostatic acid phosphatase' _entity.formula_weight 4561.464 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec 3.1.3.2 _entity.pdbx_mutation ? _entity.pdbx_fragment 'UNP residues 248-286' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name PAP # _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 GIHKQKEKSRLQGGVLVNEILNHMKRATQIPSYKKLIMY _entity_poly.pdbx_seq_one_letter_code_can GIHKQKEKSRLQGGVLVNEILNHMKRATQIPSYKKLIMY _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 ILE n 1 3 HIS n 1 4 LYS n 1 5 GLN n 1 6 LYS n 1 7 GLU n 1 8 LYS n 1 9 SER n 1 10 ARG n 1 11 LEU n 1 12 GLN n 1 13 GLY n 1 14 GLY n 1 15 VAL n 1 16 LEU n 1 17 VAL n 1 18 ASN n 1 19 GLU n 1 20 ILE n 1 21 LEU n 1 22 ASN n 1 23 HIS n 1 24 MET n 1 25 LYS n 1 26 ARG n 1 27 ALA n 1 28 THR n 1 29 GLN n 1 30 ILE n 1 31 PRO n 1 32 SER n 1 33 TYR n 1 34 LYS n 1 35 LYS n 1 36 LEU n 1 37 ILE n 1 38 MET n 1 39 TYR 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 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'purchased from from a vendor' # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PPAP_HUMAN _struct_ref.pdbx_db_accession P15309 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GIHKQKEKSRLQGGVLVNEILNHMKRATQIPSYKKLIMY _struct_ref.pdbx_align_begin 248 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2L77 _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 39 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P15309 _struct_ref_seq.db_align_beg 248 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 286 _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 39 # 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 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 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-1H TOCSY' 1 2 1 '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 7.5 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '1.2 mM PAP248-286-1; 20 mM sodium phosphate-2; 10 % [U-99% 2H] D2O-3; 50 % [U-99% 2H] TFE-4; trifluoroethanol/water' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system trifluoroethanol/water # _pdbx_nmr_spectrometer.field_strength 900 _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 2L77 _pdbx_nmr_refine.method 'torsion angle dynamics, simulated annealing' _pdbx_nmr_refine.details ? _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 'target function' _pdbx_nmr_ensemble.conformers_calculated_total_number 1000 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2L77 _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.representative_conformer 1 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2L77 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Cornilescu, Delaglio and Bax' refinement TALOS ? 1 'Guntert, Mumenthaler and Wuthrich' 'structure solution' CYANA ? 2 'Guntert, Mumenthaler and Wuthrich' refinement CYANA ? 3 'Koradi, Billeter and Wuthrich' 'structure solution' Molmol ? 4 Goddard 'chemical shift assignment' SPARKY ? 5 Goddard 'data analysis' SPARKY ? 6 'Laskowski and MacArthur' 'data analysis' ProcheckNMR ? 7 'Laskowski and MacArthur' 'structure solution' ProcheckNMR ? 8 'Bruker Biospin' collection TOPSPIN ? 9 'Bruker Biospin' processing TOPSPIN ? 10 # _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 2L77 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2L77 _struct.title 'Solution NMR structure of PAP248-286 in 50% TFE' _struct.pdbx_descriptor 'Prostatic acid phosphatase (E.C.3.1.3.2)' _struct.pdbx_model_details 'fewest violations, model 1' _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2L77 _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'PAP248-286, SEVI, AMYLOID, 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_biol.details ? # 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 GLN A 5 ? SER A 9 ? GLN A 5 SER A 9 5 ? 5 HELX_P HELX_P2 2 LEU A 11 ? ILE A 30 ? LEU A 11 ILE A 30 1 ? 20 HELX_P HELX_P3 3 SER A 32 ? MET A 38 ? SER A 32 MET A 38 1 ? 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2L77 _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 1 1 GLY GLY A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 HIS 3 3 3 HIS HIS A . n A 1 4 LYS 4 4 4 LYS LYS A . n A 1 5 GLN 5 5 5 GLN GLN A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 GLU 7 7 7 GLU GLU A . n A 1 8 LYS 8 8 8 LYS LYS A . n A 1 9 SER 9 9 9 SER SER A . n A 1 10 ARG 10 10 10 ARG ARG A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 GLN 12 12 12 GLN GLN A . n A 1 13 GLY 13 13 13 GLY GLY A . n A 1 14 GLY 14 14 14 GLY GLY A . n A 1 15 VAL 15 15 15 VAL VAL A . n A 1 16 LEU 16 16 16 LEU LEU A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 ASN 18 18 18 ASN ASN A . n A 1 19 GLU 19 19 19 GLU GLU A . n A 1 20 ILE 20 20 20 ILE ILE A . n A 1 21 LEU 21 21 21 LEU LEU A . n A 1 22 ASN 22 22 22 ASN ASN A . n A 1 23 HIS 23 23 23 HIS HIS A . n A 1 24 MET 24 24 24 MET MET A . n A 1 25 LYS 25 25 25 LYS LYS A . n A 1 26 ARG 26 26 26 ARG ARG A . n A 1 27 ALA 27 27 27 ALA ALA A . n A 1 28 THR 28 28 28 THR THR A . n A 1 29 GLN 29 29 29 GLN GLN A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 PRO 31 31 31 PRO PRO A . n A 1 32 SER 32 32 32 SER SER A . n A 1 33 TYR 33 33 33 TYR TYR A . n A 1 34 LYS 34 34 34 LYS LYS A . n A 1 35 LYS 35 35 35 LYS LYS A . n A 1 36 LEU 36 36 36 LEU LEU A . n A 1 37 ILE 37 37 37 ILE ILE A . n A 1 38 MET 38 38 38 MET MET A . n A 1 39 TYR 39 39 39 TYR TYR 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 2010-12-29 2 'Structure model' 1 1 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 ? # _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 'Version format compliance' # 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 PAP248-286-1 1.2 ? mM ? 1 'sodium phosphate-2' 20 ? mM ? 1 D2O-3 10 ? % '[U-99% 2H]' 1 TFE-4 50 ? % '[U-99% 2H]' 1 # 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 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 2 2 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 3 3 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 4 4 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 5 5 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 6 6 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.499 1.229 0.270 0.019 N 7 7 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 8 8 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 9 9 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 N 10 10 C A TYR 39 ? ? OXT A TYR 39 ? ? 1.500 1.229 0.271 0.019 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 ILE A 2 ? ? -142.68 20.97 2 1 ARG A 10 ? ? -93.35 -74.23 3 1 PRO A 31 ? ? -69.83 2.26 4 2 PRO A 31 ? ? -69.74 1.56 5 3 PRO A 31 ? ? -69.64 0.90 6 4 LYS A 4 ? ? 178.60 -179.68 7 4 ARG A 10 ? ? -119.58 -74.55 8 4 PRO A 31 ? ? -69.75 2.15 9 5 HIS A 3 ? ? -94.31 42.13 10 5 PRO A 31 ? ? -69.79 0.69 11 6 GLN A 5 ? ? -146.73 -45.47 12 6 SER A 9 ? ? -92.17 -72.40 13 6 PRO A 31 ? ? -69.71 0.68 14 6 MET A 38 ? ? -111.66 -169.32 15 7 HIS A 3 ? ? -61.94 -177.70 16 7 LYS A 4 ? ? -120.72 -169.74 17 7 ARG A 10 ? ? -82.94 -72.11 18 7 PRO A 31 ? ? -69.71 1.63 19 9 PRO A 31 ? ? -69.82 1.98 20 10 ARG A 10 ? ? -109.98 -73.17 21 10 PRO A 31 ? ? -69.68 1.58 22 10 MET A 38 ? ? -58.12 -179.09 #