data_wwPDB_remediated_restraints_file_for_PDB_entry_1clh # This wwPDB archive file contains, for PDB entry 1clh: # # - 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, W Vranken, C Penkett, J Lin, CF Schulte, G Vuister, G Vriend, # JL Markley, EL Ulrich. BioMagResBank database `NMR Restraints Grid` with # curated sets of experimental NMR restraints for over 4,000 protein and nucleic # acid PDB entries. (in preparation) save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_1clh _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1clh" _Entry.NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Details "Contains the remediated restraint lists and coordinates for PDB entry 1clh" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1clh _Assembly.ID 1 _Assembly.Name 1clh _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 18078.3973 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 CYCLOPHILIN 1 $CYCLOPHILIN A . no . . . . . . rr_1clh 1 stop_ save_ save_CYCLOPHILIN _Entity.Sf_category entity _Entity.Sf_framecode CYCLOPHILIN _Entity.Entry_ID rr_1clh _Entity.ID 1 _Entity.Name CYCLOPHILIN _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; AKGDPHVLLTTSAGNIELEL DKQKAPVSVQNFVDYVNSGF YNNTTFHRVIPGFMIQGGGF TEQMQQKKPNPPIKNEADNG LRNTRGTIAMARTADKDSAT SQFFINVADNAFLDHGQRDF GYAVFGKVVKGMDVADKISQ VPTHDVGPYQNVPSKPVVIL SAKVLP ; _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 166 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 18078.3973 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 . ALA . rr_1clh 1 2 . LYS . rr_1clh 1 3 . GLY . rr_1clh 1 4 . ASP . rr_1clh 1 5 . PRO . rr_1clh 1 6 . HIS . rr_1clh 1 7 . VAL . rr_1clh 1 8 . LEU . rr_1clh 1 9 . LEU . rr_1clh 1 10 . THR . rr_1clh 1 11 . THR . rr_1clh 1 12 . SER . rr_1clh 1 13 . ALA . rr_1clh 1 14 . GLY . rr_1clh 1 15 . ASN . rr_1clh 1 16 . ILE . rr_1clh 1 17 . GLU . rr_1clh 1 18 . LEU . rr_1clh 1 19 . GLU . rr_1clh 1 20 . LEU . rr_1clh 1 21 . ASP . rr_1clh 1 22 . LYS . rr_1clh 1 23 . GLN . rr_1clh 1 24 . LYS . rr_1clh 1 25 . ALA . rr_1clh 1 26 . PRO . rr_1clh 1 27 . VAL . rr_1clh 1 28 . SER . rr_1clh 1 29 . VAL . rr_1clh 1 30 . GLN . rr_1clh 1 31 . ASN . rr_1clh 1 32 . PHE . rr_1clh 1 33 . VAL . rr_1clh 1 34 . ASP . rr_1clh 1 35 . TYR . rr_1clh 1 36 . VAL . rr_1clh 1 37 . ASN . rr_1clh 1 38 . SER . rr_1clh 1 39 . GLY . rr_1clh 1 40 . PHE . rr_1clh 1 41 . TYR . rr_1clh 1 42 . ASN . rr_1clh 1 43 . ASN . rr_1clh 1 44 . THR . rr_1clh 1 45 . THR . rr_1clh 1 46 . PHE . rr_1clh 1 47 . HIS . rr_1clh 1 48 . ARG . rr_1clh 1 49 . VAL . rr_1clh 1 50 . ILE . rr_1clh 1 51 . PRO . rr_1clh 1 52 . GLY . rr_1clh 1 53 . PHE . rr_1clh 1 54 . MET . rr_1clh 1 55 . ILE . rr_1clh 1 56 . GLN . rr_1clh 1 57 . GLY . rr_1clh 1 58 . GLY . rr_1clh 1 59 . GLY . rr_1clh 1 60 . PHE . rr_1clh 1 61 . THR . rr_1clh 1 62 . GLU . rr_1clh 1 63 . GLN . rr_1clh 1 64 . MET . rr_1clh 1 65 . GLN . rr_1clh 1 66 . GLN . rr_1clh 1 67 . LYS . rr_1clh 1 68 . LYS . rr_1clh 1 69 . PRO . rr_1clh 1 70 . ASN . rr_1clh 1 71 . PRO . rr_1clh 1 72 . PRO . rr_1clh 1 73 . ILE . rr_1clh 1 74 . LYS . rr_1clh 1 75 . ASN . rr_1clh 1 76 . GLU . rr_1clh 1 77 . ALA . rr_1clh 1 78 . ASP . rr_1clh 1 79 . ASN . rr_1clh 1 80 . GLY . rr_1clh 1 81 . LEU . rr_1clh 1 82 . ARG . rr_1clh 1 83 . ASN . rr_1clh 1 84 . THR . rr_1clh 1 85 . ARG . rr_1clh 1 86 . GLY . rr_1clh 1 87 . THR . rr_1clh 1 88 . ILE . rr_1clh 1 89 . ALA . rr_1clh 1 90 . MET . rr_1clh 1 91 . ALA . rr_1clh 1 92 . ARG . rr_1clh 1 93 . THR . rr_1clh 1 94 . ALA . rr_1clh 1 95 . ASP . rr_1clh 1 96 . LYS . rr_1clh 1 97 . ASP . rr_1clh 1 98 . SER . rr_1clh 1 99 . ALA . rr_1clh 1 100 . THR . rr_1clh 1 101 . SER . rr_1clh 1 102 . GLN . rr_1clh 1 103 . PHE . rr_1clh 1 104 . PHE . rr_1clh 1 105 . ILE . rr_1clh 1 106 . ASN . rr_1clh 1 107 . VAL . rr_1clh 1 108 . ALA . rr_1clh 1 109 . ASP . rr_1clh 1 110 . ASN . rr_1clh 1 111 . ALA . rr_1clh 1 112 . PHE . rr_1clh 1 113 . LEU . rr_1clh 1 114 . ASP . rr_1clh 1 115 . HIS . rr_1clh 1 116 . GLY . rr_1clh 1 117 . GLN . rr_1clh 1 118 . ARG . rr_1clh 1 119 . ASP . rr_1clh 1 120 . PHE . rr_1clh 1 121 . GLY . rr_1clh 1 122 . TYR . rr_1clh 1 123 . ALA . rr_1clh 1 124 . VAL . rr_1clh 1 125 . PHE . rr_1clh 1 126 . GLY . rr_1clh 1 127 . LYS . rr_1clh 1 128 . VAL . rr_1clh 1 129 . VAL . rr_1clh 1 130 . LYS . rr_1clh 1 131 . GLY . rr_1clh 1 132 . MET . rr_1clh 1 133 . ASP . rr_1clh 1 134 . VAL . rr_1clh 1 135 . ALA . rr_1clh 1 136 . ASP . rr_1clh 1 137 . LYS . rr_1clh 1 138 . ILE . rr_1clh 1 139 . SER . rr_1clh 1 140 . GLN . rr_1clh 1 141 . VAL . rr_1clh 1 142 . PRO . rr_1clh 1 143 . THR . rr_1clh 1 144 . HIS . rr_1clh 1 145 . ASP . rr_1clh 1 146 . VAL . rr_1clh 1 147 . GLY . rr_1clh 1 148 . PRO . rr_1clh 1 149 . TYR . rr_1clh 1 150 . GLN . rr_1clh 1 151 . ASN . rr_1clh 1 152 . VAL . rr_1clh 1 153 . PRO . rr_1clh 1 154 . SER . rr_1clh 1 155 . LYS . rr_1clh 1 156 . PRO . rr_1clh 1 157 . VAL . rr_1clh 1 158 . VAL . rr_1clh 1 159 . ILE . rr_1clh 1 160 . LEU . rr_1clh 1 161 . SER . rr_1clh 1 162 . ALA . rr_1clh 1 163 . LYS . rr_1clh 1 164 . VAL . rr_1clh 1 165 . LEU . rr_1clh 1 166 . PRO . rr_1clh 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 . ALA 1 1 rr_1clh 1 . LYS 2 2 rr_1clh 1 . GLY 3 3 rr_1clh 1 . ASP 4 4 rr_1clh 1 . PRO 5 5 rr_1clh 1 . HIS 6 6 rr_1clh 1 . VAL 7 7 rr_1clh 1 . LEU 8 8 rr_1clh 1 . LEU 9 9 rr_1clh 1 . THR 10 10 rr_1clh 1 . THR 11 11 rr_1clh 1 . SER 12 12 rr_1clh 1 . ALA 13 13 rr_1clh 1 . GLY 14 14 rr_1clh 1 . ASN 15 15 rr_1clh 1 . ILE 16 16 rr_1clh 1 . GLU 17 17 rr_1clh 1 . LEU 18 18 rr_1clh 1 . GLU 19 19 rr_1clh 1 . LEU 20 20 rr_1clh 1 . ASP 21 21 rr_1clh 1 . LYS 22 22 rr_1clh 1 . GLN 23 23 rr_1clh 1 . LYS 24 24 rr_1clh 1 . ALA 25 25 rr_1clh 1 . PRO 26 26 rr_1clh 1 . VAL 27 27 rr_1clh 1 . SER 28 28 rr_1clh 1 . VAL 29 29 rr_1clh 1 . GLN 30 30 rr_1clh 1 . ASN 31 31 rr_1clh 1 . PHE 32 32 rr_1clh 1 . VAL 33 33 rr_1clh 1 . ASP 34 34 rr_1clh 1 . TYR 35 35 rr_1clh 1 . VAL 36 36 rr_1clh 1 . ASN 37 37 rr_1clh 1 . SER 38 38 rr_1clh 1 . GLY 39 39 rr_1clh 1 . PHE 40 40 rr_1clh 1 . TYR 41 41 rr_1clh 1 . ASN 42 42 rr_1clh 1 . ASN 43 43 rr_1clh 1 . THR 44 44 rr_1clh 1 . THR 45 45 rr_1clh 1 . PHE 46 46 rr_1clh 1 . HIS 47 47 rr_1clh 1 . ARG 48 48 rr_1clh 1 . VAL 49 49 rr_1clh 1 . ILE 50 50 rr_1clh 1 . PRO 51 51 rr_1clh 1 . GLY 52 52 rr_1clh 1 . PHE 53 53 rr_1clh 1 . MET 54 54 rr_1clh 1 . ILE 55 55 rr_1clh 1 . GLN 56 56 rr_1clh 1 . GLY 57 57 rr_1clh 1 . GLY 58 58 rr_1clh 1 . GLY 59 59 rr_1clh 1 . PHE 60 60 rr_1clh 1 . THR 61 61 rr_1clh 1 . GLU 62 62 rr_1clh 1 . GLN 63 63 rr_1clh 1 . MET 64 64 rr_1clh 1 . GLN 65 65 rr_1clh 1 . GLN 66 66 rr_1clh 1 . LYS 67 67 rr_1clh 1 . LYS 68 68 rr_1clh 1 . PRO 69 69 rr_1clh 1 . ASN 70 70 rr_1clh 1 . PRO 71 71 rr_1clh 1 . PRO 72 72 rr_1clh 1 . ILE 73 73 rr_1clh 1 . LYS 74 74 rr_1clh 1 . ASN 75 75 rr_1clh 1 . GLU 76 76 rr_1clh 1 . ALA 77 77 rr_1clh 1 . ASP 78 78 rr_1clh 1 . ASN 79 79 rr_1clh 1 . GLY 80 80 rr_1clh 1 . LEU 81 81 rr_1clh 1 . ARG 82 82 rr_1clh 1 . ASN 83 83 rr_1clh 1 . THR 84 84 rr_1clh 1 . ARG 85 85 rr_1clh 1 . GLY 86 86 rr_1clh 1 . THR 87 87 rr_1clh 1 . ILE 88 88 rr_1clh 1 . ALA 89 89 rr_1clh 1 . MET 90 90 rr_1clh 1 . ALA 91 91 rr_1clh 1 . ARG 92 92 rr_1clh 1 . THR 93 93 rr_1clh 1 . ALA 94 94 rr_1clh 1 . ASP 95 95 rr_1clh 1 . LYS 96 96 rr_1clh 1 . ASP 97 97 rr_1clh 1 . SER 98 98 rr_1clh 1 . ALA 99 99 rr_1clh 1 . THR 100 100 rr_1clh 1 . SER 101 101 rr_1clh 1 . GLN 102 102 rr_1clh 1 . PHE 103 103 rr_1clh 1 . PHE 104 104 rr_1clh 1 . ILE 105 105 rr_1clh 1 . ASN 106 106 rr_1clh 1 . VAL 107 107 rr_1clh 1 . ALA 108 108 rr_1clh 1 . ASP 109 109 rr_1clh 1 . ASN 110 110 rr_1clh 1 . ALA 111 111 rr_1clh 1 . PHE 112 112 rr_1clh 1 . LEU 113 113 rr_1clh 1 . ASP 114 114 rr_1clh 1 . HIS 115 115 rr_1clh 1 . GLY 116 116 rr_1clh 1 . GLN 117 117 rr_1clh 1 . ARG 118 118 rr_1clh 1 . ASP 119 119 rr_1clh 1 . PHE 120 120 rr_1clh 1 . GLY 121 121 rr_1clh 1 . TYR 122 122 rr_1clh 1 . ALA 123 123 rr_1clh 1 . VAL 124 124 rr_1clh 1 . PHE 125 125 rr_1clh 1 . GLY 126 126 rr_1clh 1 . LYS 127 127 rr_1clh 1 . VAL 128 128 rr_1clh 1 . VAL 129 129 rr_1clh 1 . LYS 130 130 rr_1clh 1 . GLY 131 131 rr_1clh 1 . MET 132 132 rr_1clh 1 . ASP 133 133 rr_1clh 1 . VAL 134 134 rr_1clh 1 . ALA 135 135 rr_1clh 1 . ASP 136 136 rr_1clh 1 . LYS 137 137 rr_1clh 1 . ILE 138 138 rr_1clh 1 . SER 139 139 rr_1clh 1 . GLN 140 140 rr_1clh 1 . VAL 141 141 rr_1clh 1 . PRO 142 142 rr_1clh 1 . THR 143 143 rr_1clh 1 . HIS 144 144 rr_1clh 1 . ASP 145 145 rr_1clh 1 . VAL 146 146 rr_1clh 1 . GLY 147 147 rr_1clh 1 . PRO 148 148 rr_1clh 1 . TYR 149 149 rr_1clh 1 . GLN 150 150 rr_1clh 1 . ASN 151 151 rr_1clh 1 . VAL 152 152 rr_1clh 1 . PRO 153 153 rr_1clh 1 . SER 154 154 rr_1clh 1 . LYS 155 155 rr_1clh 1 . PRO 156 156 rr_1clh 1 . VAL 157 157 rr_1clh 1 . VAL 158 158 rr_1clh 1 . ILE 159 159 rr_1clh 1 . LEU 160 160 rr_1clh 1 . SER 161 161 rr_1clh 1 . ALA 162 162 rr_1clh 1 . LYS 163 163 rr_1clh 1 . VAL 164 164 rr_1clh 1 . LEU 165 165 rr_1clh 1 . PRO 166 166 rr_1clh 1 stop_ save_ save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_1clh _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 12 save_ save_global_Org_file_characteristics _Constraint_stat_list.Sf_framecode global_Org_file_characteristics _Constraint_stat_list.Sf_category constraint_statistics _Constraint_stat_list.Entry_ID rr_1clh _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 1clh.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1clh 1 1 1clh.mr . . unknown 2 distance NOE simple 0 rr_1clh 1 1 1clh.mr . . n/a 3 comment "Not applicable" "Not applicable" 0 rr_1clh 1 1 1clh.mr . . unknown 4 distance "hydrogen bond" simple 0 rr_1clh 1 1 1clh.mr . . n/a 5 comment "Not applicable" "Not applicable" 0 rr_1clh 1 1 1clh.mr . . unknown 6 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1clh 1 1 1clh.mr . . "MR format" 7 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1clh 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_1clh _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 ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS) 20-DEC-93 1CLH *COMPND CYCLOPHILIN (NMR, 12 STRUCTURES) *SOURCE (ESCHERICHIA COLI) *AUTHOR R.T.CLUBB,G.WAGNER *REVDAT 1 31-MAY-94 1CLH 0 ############################################################################## SUPPLEMENTARY MATERIAL Experimental NMR restraints used to determine the three-dimensional solution structure of periplasmic Cyclophilin from E. coli. The structures are based on 1458 interproton distance restraints derived from NOE measurements; 108 hydrogen-bonding distance restraints for 54 hydrogen-bonds identified on the basis of the NOE and amide proton exchange data, as well as initial structure calculations; and 101 phi and 53 chi1 torsion angle restraints derived from coupling constants and NOE data. All the coordinates are included as a separate file: ecyp_brookhaven.pdb References 1. Clubb, R. T., Ferguson, S. B., Walsh, C. T., and Wagner, G. (1994) Biochemistry, in press ############################################################################## NOE RESTRAINTS 1458 Total 483 (|i-j|) = 1 149 (|i-j|) =< 4 574 (|i-j|) > 4 252 Intraresidual ("-1.0" indicates a lower bound equal to the sum of the van der Waals radii) ############################################################################## Bounds Residue Atom Residue Atom Lower(A) Upper(A) ############################################################################## ; save_ save_MR_file_comment_5 _Org_constr_file_comment.Sf_framecode MR_file_comment_5 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_1clh _Org_constr_file_comment.ID 3 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 5 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; ############################################################################## DIHEDRAL ANGLE RESTRAINTS 154 Total 101 Phi 53 Chi1 ############################################################################## Bounds Residue Atom Residue Atom Residue Atom Residue Atom Lower Upper ############################################################################## ; save_ save_MR_file_comment_3 _Org_constr_file_comment.Sf_framecode MR_file_comment_3 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_1clh _Org_constr_file_comment.ID 2 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 3 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; ############################################################################## HYDROGEN BOND RESTRAINTS 108 Total for 54 hydrogen-bonds ############################################################################## Bounds Residue Atom Residue Atom Lower(A) Upper(A) ############################################################################## ; save_