data_wwPDB_remediated_restraints_file_for_PDB_entry_2m7y # This wwPDB archive file contains, for PDB entry 2m7y: # # - Sequence information from the PDB mmCIF file # - NMR restraints from the PDB MR file # # In this file, the NMR restraints share the same atom names as in the coordinate # file, and in this way can differ from the data deposited at the wwPDB. To achieve # this aim, the NMR restraints were parsed from their original format files, and # the coordinates and NMR restraints information were subsequently harmonized. # # Due to the complexity of this harmonization process, minor modifications could # have occurred to the NMR restraints information, or data could have been lost # because of parsing or conversion errors. The PDB file remains the # authoritative reference for the atomic coordinates and the originally deposited # restraints files remain the primary reference for these data. # # This file is generated as part of the wwPDB at the BioMagResBank (BMRB) in # collaboration with the PDBe (formerly MSD) group at the European # Bioinformatics Institute (EBI) and the CMBI/IMM group at the Radboud # University of Nijmegen. # # Several software packages were used to produce this file: # # - Wattos (BMRB and CMBI/IMM). # - FormatConverter and NMRStarExport (PDBe). # - CCPN framework (http://www.ccpn.ac.uk/). # # More information about this process can be found in the references below. # Please cite the original reference for this PDB entry. # # JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL # Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED # containing converted and filtered sets of experimental NMR restraints and # coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12. # # WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL # Markley, J Ionides, ED Laue (2005). The CCPN data model for NMR spectroscopy: # development of a software pipeline. Proteins 59, 687-696. # # JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, # G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for # 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389-396. ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_2m7y _Entry.Title 'wwPDB remediated NMR restraints for PDB entry 2m7y' _Entry.Version_type original _Entry.NMR_STAR_version 3.1.0.8 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Details 'Contains the remediated restraint lists and coordinates for PDB entry 2m7y' _Entry.PDB_coordinate_file_version 3.20 loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID PDB 2m7y 'Master copy' rr_2m7y stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_2m7y _Assembly.ID 1 _Assembly.Name 2m7y _Assembly.Number_of_components 2 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 1 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state 'all free' _Assembly.Molecular_mass 8324.4549 loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 'Leader peptide' 1 $Leader_peptide A . no . . . . . . rr_2m7y 1 2 'ZINC ION' 2 $ZINC_ION B . no . . . . . . rr_2m7y 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_Leader_peptide _Entity.Sf_category entity _Entity.Sf_framecode Leader_peptide _Entity.Entry_ID rr_2m7y _Entity.ID 1 _Entity.Name Leader_peptide _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; GSTAMATTMEQEICAHSMTF EECPKCSALQYRNGFYLLKY DEEWYPEELLTDGEDDVFDP DLDMEVVFETQ ; _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Number_of_monomers 71 _Entity.Paramagnetic no _Entity.Thiol_state 'all free' _Entity.Parent_entity_ID 1 _Entity.Formula_weight 8259.0749 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . GLY . rr_2m7y 1 2 . SER . rr_2m7y 1 3 . THR . rr_2m7y 1 4 . ALA . rr_2m7y 1 5 . MET . rr_2m7y 1 6 . ALA . rr_2m7y 1 7 . THR . rr_2m7y 1 8 . THR . rr_2m7y 1 9 . MET . rr_2m7y 1 10 . GLU . rr_2m7y 1 11 . GLN . rr_2m7y 1 12 . GLU . rr_2m7y 1 13 . ILE . rr_2m7y 1 14 . CYS . rr_2m7y 1 15 . ALA . rr_2m7y 1 16 . HIS . rr_2m7y 1 17 . SER . rr_2m7y 1 18 . MET . rr_2m7y 1 19 . THR . rr_2m7y 1 20 . PHE . rr_2m7y 1 21 . GLU . rr_2m7y 1 22 . GLU . rr_2m7y 1 23 . CYS . rr_2m7y 1 24 . PRO . rr_2m7y 1 25 . LYS . rr_2m7y 1 26 . CYS . rr_2m7y 1 27 . SER . rr_2m7y 1 28 . ALA . rr_2m7y 1 29 . LEU . rr_2m7y 1 30 . GLN . rr_2m7y 1 31 . TYR . rr_2m7y 1 32 . ARG . rr_2m7y 1 33 . ASN . rr_2m7y 1 34 . GLY . rr_2m7y 1 35 . PHE . rr_2m7y 1 36 . TYR . rr_2m7y 1 37 . LEU . rr_2m7y 1 38 . LEU . rr_2m7y 1 39 . LYS . rr_2m7y 1 40 . TYR . rr_2m7y 1 41 . ASP . rr_2m7y 1 42 . GLU . rr_2m7y 1 43 . GLU . rr_2m7y 1 44 . TRP . rr_2m7y 1 45 . TYR . rr_2m7y 1 46 . PRO . rr_2m7y 1 47 . GLU . rr_2m7y 1 48 . GLU . rr_2m7y 1 49 . LEU . rr_2m7y 1 50 . LEU . rr_2m7y 1 51 . THR . rr_2m7y 1 52 . ASP . rr_2m7y 1 53 . GLY . rr_2m7y 1 54 . GLU . rr_2m7y 1 55 . ASP . rr_2m7y 1 56 . ASP . rr_2m7y 1 57 . VAL . rr_2m7y 1 58 . PHE . rr_2m7y 1 59 . ASP . rr_2m7y 1 60 . PRO . rr_2m7y 1 61 . ASP . rr_2m7y 1 62 . LEU . rr_2m7y 1 63 . ASP . rr_2m7y 1 64 . MET . rr_2m7y 1 65 . GLU . rr_2m7y 1 66 . VAL . rr_2m7y 1 67 . VAL . rr_2m7y 1 68 . PHE . rr_2m7y 1 69 . GLU . rr_2m7y 1 70 . THR . rr_2m7y 1 71 . GLN . rr_2m7y 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . GLY 1 1 rr_2m7y 1 . SER 2 2 rr_2m7y 1 . THR 3 3 rr_2m7y 1 . ALA 4 4 rr_2m7y 1 . MET 5 5 rr_2m7y 1 . ALA 6 6 rr_2m7y 1 . THR 7 7 rr_2m7y 1 . THR 8 8 rr_2m7y 1 . MET 9 9 rr_2m7y 1 . GLU 10 10 rr_2m7y 1 . GLN 11 11 rr_2m7y 1 . GLU 12 12 rr_2m7y 1 . ILE 13 13 rr_2m7y 1 . CYS 14 14 rr_2m7y 1 . ALA 15 15 rr_2m7y 1 . HIS 16 16 rr_2m7y 1 . SER 17 17 rr_2m7y 1 . MET 18 18 rr_2m7y 1 . THR 19 19 rr_2m7y 1 . PHE 20 20 rr_2m7y 1 . GLU 21 21 rr_2m7y 1 . GLU 22 22 rr_2m7y 1 . CYS 23 23 rr_2m7y 1 . PRO 24 24 rr_2m7y 1 . LYS 25 25 rr_2m7y 1 . CYS 26 26 rr_2m7y 1 . SER 27 27 rr_2m7y 1 . ALA 28 28 rr_2m7y 1 . LEU 29 29 rr_2m7y 1 . GLN 30 30 rr_2m7y 1 . TYR 31 31 rr_2m7y 1 . ARG 32 32 rr_2m7y 1 . ASN 33 33 rr_2m7y 1 . GLY 34 34 rr_2m7y 1 . PHE 35 35 rr_2m7y 1 . TYR 36 36 rr_2m7y 1 . LEU 37 37 rr_2m7y 1 . LEU 38 38 rr_2m7y 1 . LYS 39 39 rr_2m7y 1 . TYR 40 40 rr_2m7y 1 . ASP 41 41 rr_2m7y 1 . GLU 42 42 rr_2m7y 1 . GLU 43 43 rr_2m7y 1 . TRP 44 44 rr_2m7y 1 . TYR 45 45 rr_2m7y 1 . PRO 46 46 rr_2m7y 1 . GLU 47 47 rr_2m7y 1 . GLU 48 48 rr_2m7y 1 . LEU 49 49 rr_2m7y 1 . LEU 50 50 rr_2m7y 1 . THR 51 51 rr_2m7y 1 . ASP 52 52 rr_2m7y 1 . GLY 53 53 rr_2m7y 1 . GLU 54 54 rr_2m7y 1 . ASP 55 55 rr_2m7y 1 . ASP 56 56 rr_2m7y 1 . VAL 57 57 rr_2m7y 1 . PHE 58 58 rr_2m7y 1 . ASP 59 59 rr_2m7y 1 . PRO 60 60 rr_2m7y 1 . ASP 61 61 rr_2m7y 1 . LEU 62 62 rr_2m7y 1 . ASP 63 63 rr_2m7y 1 . MET 64 64 rr_2m7y 1 . GLU 65 65 rr_2m7y 1 . VAL 66 66 rr_2m7y 1 . VAL 67 67 rr_2m7y 1 . PHE 68 68 rr_2m7y 1 . GLU 69 69 rr_2m7y 1 . THR 70 70 rr_2m7y 1 . GLN 71 71 rr_2m7y 1 stop_ save_ save_ZINC_ION _Entity.Sf_category entity _Entity.Sf_framecode ZINC_ION _Entity.Entry_ID rr_2m7y _Entity.ID 2 _Entity.Name ZINC_ION _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_chirality yes _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID ZN _Entity.Number_of_monomers 1 _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Parent_entity_ID 2 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . ZN . rr_2m7y 2 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_ZN _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_ZN _Chem_comp.Entry_ID rr_2m7y _Chem_comp.ID ZN _Chem_comp.Name 'ZINC ION' _Chem_comp.Type non-polymer _Chem_comp.PDB_code ZN _Chem_comp.Formal_charge 2 _Chem_comp.Paramagnetic no _Chem_comp.Aromatic no _Chem_comp.Formula Zn _Chem_comp.Formula_weight 65.38 save_ ############################## # Structure determinations # ############################## ########################## # Conformer statistics # ########################## save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_2m7y _Conformer_stat_list.ID 1 _Conformer_stat_list.Conf_family_coord_set_ID 1 _Conformer_stat_list.Conf_family_coord_set_label $Original_constraints_and_structures _Conformer_stat_list.Conformer_submitted_total_num 1 save_ ########################### # Constraint Statistics # ########################### save_constraint_statistics _Constraint_stat_list.Sf_framecode constraint_statistics _Constraint_stat_list.Sf_category constraint_statistics _Constraint_stat_list.Entry_ID rr_2m7y _Constraint_stat_list.ID 1 loop_ _Constraint_file.ID _Constraint_file.Constraint_filename _Constraint_file.Software_ID _Constraint_file.Software_label _Constraint_file.Software_name _Constraint_file.Block_ID _Constraint_file.Constraint_type _Constraint_file.Constraint_subtype _Constraint_file.Constraint_subsubtype _Constraint_file.Constraint_number _Constraint_file.Entry_ID _Constraint_file.Constraint_stat_list_ID 1 2m7y.mr . . 'MR format' 1 comment 'Not applicable' 'Not applicable' 0 rr_2m7y 1 1 2m7y.mr . . XPLOR/CNS 2 'dihedral angle' 'Not applicable' 'Not applicable' 20 rr_2m7y 1 1 2m7y.mr . . 'MR format' 3 'nomenclature mapping' 'Not applicable' 'Not applicable' 0 rr_2m7y 1 stop_ save_ save_CNS/XPLOR_dihedral_2 _Torsion_angle_constraint_list.Sf_category torsion_angle_constraints _Torsion_angle_constraint_list.Sf_framecode CNS/XPLOR_dihedral_2 _Torsion_angle_constraint_list.Entry_ID rr_2m7y _Torsion_angle_constraint_list.ID 1 _Torsion_angle_constraint_list.Details 'Generated by Wattos' _Torsion_angle_constraint_list.Constraint_file_ID 1 _Torsion_angle_constraint_list.Block_ID 2 loop_ _Torsion_angle_constraint_software.Software_ID _Torsion_angle_constraint_software.Software_label _Torsion_angle_constraint_software.Method_ID _Torsion_angle_constraint_software.Method_label _Torsion_angle_constraint_software.Entry_ID _Torsion_angle_constraint_software.Torsion_angle_constraint_list_ID . . . . rr_2m7y 1 stop_ loop_ _TA_constraint_comment_org.ID _TA_constraint_comment_org.Comment_text _TA_constraint_comment_org.Comment_begin_line _TA_constraint_comment_org.Comment_begin_column _TA_constraint_comment_org.Comment_end_line _TA_constraint_comment_org.Comment_end_column _TA_constraint_comment_org.Entry_ID _TA_constraint_comment_org.Torsion_angle_constraint_list_ID 1 '! I13' 1 1 1 7 rr_2m7y 1 2 '! C14' 4 1 4 7 rr_2m7y 1 3 '! A15' 7 1 7 7 rr_2m7y 1 4 '! H16' 10 1 10 7 rr_2m7y 1 5 '! S17' 13 1 13 7 rr_2m7y 1 6 '! M18' 16 1 16 7 rr_2m7y 1 7 '! T19' 19 1 19 7 rr_2m7y 1 8 '! F20' 22 1 22 7 rr_2m7y 1 9 '! E21' 25 1 25 7 rr_2m7y 1 10 '! E22' 28 1 28 7 rr_2m7y 1 11 '! C23' 31 1 31 7 rr_2m7y 1 12 ; ! P24 assign (resid 23 and name C) (resid 24 and name N) (resid 24 and name CA) (resid 24 and name C) 1 -61.00 14.00 2 ! K25 ; 34 1 37 7 rr_2m7y 1 13 '! C26' 40 1 40 7 rr_2m7y 1 14 '! S27' 43 1 43 7 rr_2m7y 1 15 '! A28' 46 1 46 7 rr_2m7y 1 16 '! L29' 49 1 49 7 rr_2m7y 1 17 '! W44' 52 1 52 7 rr_2m7y 1 18 '! Y45' 55 1 55 7 rr_2m7y 1 19 ; ! P46 assign (resid 45 and name C) (resid 46 and name N) (resid 46 and name CA) (resid 46 and name C) 1 -66.00 12.00 2 ! F58 ; 58 1 61 7 rr_2m7y 1 20 '! D59' 64 1 64 7 rr_2m7y 1 stop_ loop_ _TA_constraint_conv_err.ID _TA_constraint_conv_err.Parse_file_ID _TA_constraint_conv_err.Parse_file_constraint_ID _TA_constraint_conv_err.Conv_error_type _TA_constraint_conv_err.Conv_error_note _TA_constraint_conv_err.Entry_ID _TA_constraint_conv_err.Torsion_angle_constraint_list_ID 1 2 1 1 "Not handling restraint 1, resonance(s) ' .12.C' (nmrStar names),' .13.N' (nmrStar names),' .13.CA' (nmrStar names),' .13.C' (nmrStar names) not linked" rr_2m7y 1 2 2 2 1 "Not handling restraint 2, resonance(s) ' .13.C' (nmrStar names),' .14.N' (nmrStar names),' .14.CA' (nmrStar names),' .14.C' (nmrStar names) not linked" rr_2m7y 1 3 2 3 1 "Not handling restraint 3, resonance(s) ' .14.C' (nmrStar names),' .15.N' (nmrStar names),' .15.CA' (nmrStar names),' .15.C' (nmrStar names) not linked" rr_2m7y 1 4 2 4 1 "Not handling restraint 4, resonance(s) ' .15.C' (nmrStar names),' .16.N' (nmrStar names),' .16.CA' (nmrStar names),' .16.C' (nmrStar names) not linked" rr_2m7y 1 5 2 5 1 "Not handling restraint 5, resonance(s) ' .16.C' (nmrStar names),' .17.N' (nmrStar names),' .17.CA' (nmrStar names),' .17.C' (nmrStar names) not linked" rr_2m7y 1 6 2 6 1 "Not handling restraint 6, resonance(s) ' .17.C' (nmrStar names),' .18.N' (nmrStar names),' .18.CA' (nmrStar names),' .18.C' (nmrStar names) not linked" rr_2m7y 1 7 2 7 1 "Not handling restraint 7, resonance(s) ' .18.C' (nmrStar names),' .19.N' (nmrStar names),' .19.CA' (nmrStar names),' .19.C' (nmrStar names) not linked" rr_2m7y 1 8 2 8 1 "Not handling restraint 8, resonance(s) ' .19.C' (nmrStar names),' .20.N' (nmrStar names),' .20.CA' (nmrStar names),' .20.C' (nmrStar names) not linked" rr_2m7y 1 9 2 9 1 "Not handling restraint 9, resonance(s) ' .20.C' (nmrStar names),' .21.N' (nmrStar names),' .21.CA' (nmrStar names),' .21.C' (nmrStar names) not linked" rr_2m7y 1 10 2 10 1 "Not handling restraint 10, resonance(s) ' .21.C' (nmrStar names),' .22.N' (nmrStar names),' .22.CA' (nmrStar names),' .22.C' (nmrStar names) not linked" rr_2m7y 1 11 2 11 1 "Not handling restraint 11, resonance(s) ' .22.C' (nmrStar names),' .23.N' (nmrStar names),' .23.CA' (nmrStar names),' .23.C' (nmrStar names) not linked" rr_2m7y 1 12 2 12 1 "Not handling restraint 12, resonance(s) ' .24.C' (nmrStar names),' .25.N' (nmrStar names),' .25.CA' (nmrStar names),' .25.C' (nmrStar names) not linked" rr_2m7y 1 13 2 13 1 "Not handling restraint 13, resonance(s) ' .25.C' (nmrStar names),' .26.N' (nmrStar names),' .26.CA' (nmrStar names),' .26.C' (nmrStar names) not linked" rr_2m7y 1 14 2 14 1 "Not handling restraint 14, resonance(s) ' .26.C' (nmrStar names),' .27.N' (nmrStar names),' .27.CA' (nmrStar names),' .27.C' (nmrStar names) not linked" rr_2m7y 1 15 2 15 1 "Not handling restraint 15, resonance(s) ' .27.C' (nmrStar names),' .28.N' (nmrStar names),' .28.CA' (nmrStar names),' .28.C' (nmrStar names) not linked" rr_2m7y 1 16 2 16 1 "Not handling restraint 16, resonance(s) ' .28.C' (nmrStar names),' .29.N' (nmrStar names),' .29.CA' (nmrStar names),' .29.C' (nmrStar names) not linked" rr_2m7y 1 17 2 17 1 "Not handling restraint 17, resonance(s) ' .43.C' (nmrStar names),' .44.N' (nmrStar names),' .44.CA' (nmrStar names),' .44.C' (nmrStar names) not linked" rr_2m7y 1 18 2 18 1 "Not handling restraint 18, resonance(s) ' .44.C' (nmrStar names),' .45.N' (nmrStar names),' .45.CA' (nmrStar names),' .45.C' (nmrStar names) not linked" rr_2m7y 1 19 2 19 1 "Not handling restraint 19, resonance(s) ' .57.C' (nmrStar names),' .58.N' (nmrStar names),' .58.CA' (nmrStar names),' .58.C' (nmrStar names) not linked" rr_2m7y 1 20 2 20 1 "Not handling restraint 20, resonance(s) ' .58.C' (nmrStar names),' .59.N' (nmrStar names),' .59.CA' (nmrStar names),' .59.C' (nmrStar names) not linked" rr_2m7y 1 stop_ save_ save_MR_file_comment_1 _Org_constr_file_comment.Sf_framecode MR_file_comment_1 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_2m7y _Org_constr_file_comment.ID 1 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 1 _Org_constr_file_comment.Details 'Generated by Wattos' _Org_constr_file_comment.Comment '*HEADER VIRAL PROTEIN 02-MAY-13 2M7Y *TITLE THE MENGOVIRUS LEADER PROTEIN *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: LEADER PEPTIDE; *COMPND 3 CHAIN: A; *COMPND 4 ENGINEERED: YES *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: MENGO VIRUS; *SOURCE 3 ORGANISM_TAXID: 12107; *SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; *SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; *SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET41B *KEYWDS CARDIOVIRUS, VIRAL PROTEIN *EXPDTA SOLUTION NMR *NUMMDL 1 *AUTHOR C.C.CORNILESCU, F.W.PORTER, K.Q.ZHAO, V.DAVIS, A.C.PALMENBERG, *AUTHOR 2 J.L.MARKLEY *REVDAT 1 23-OCT-13 2M7Y 0' save_