data_wwPDB_remediated_restraints_file_for_PDB_entry_1eii # This wwPDB archive file contains, for PDB entry 1eii: # # - 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. save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_1eii _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1eii" _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 1eii" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1eii _Assembly.ID 1 _Assembly.Name 1eii _Assembly.Number_of_components 2 _Assembly.Organic_ligands 1 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "all free" _Assembly.Molecular_mass 15870.977 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 "CELLULAR RETINOL BINDING PROTEIN II" 1 $CELLULAR_RETINOL_BINDING_PROTEIN_II A . no . . . . . . rr_1eii 1 2 RETINOL 2 $RETINOL B . no . . . . . . rr_1eii 1 stop_ save_ save_CELLULAR_RETINOL_BINDING_PROTEIN_II _Entity.Sf_category entity _Entity.Sf_framecode CELLULAR_RETINOL_BINDING_PROTEIN_II _Entity.Entry_ID rr_1eii _Entity.ID 1 _Entity.Name CELLULAR_RETINOL_BINDING_PROTEIN_II _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; MTKDQNGTWEMESNENFEGY MKALDIDFATRKIAVRLTQT KIIVQDGDNFKTKTNSTFRN YDLDFTVGVEFDEHTKGLDG RNVKTLVTWEGNTLVCVQKG EKENRGWKQWVEGDKLYLEL TCGDQVCRQVFKKK ; _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 134 _Entity.Paramagnetic no _Entity.Thiol_state "all free" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 15584.5206 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 . MET . rr_1eii 1 2 . THR . rr_1eii 1 3 . LYS . rr_1eii 1 4 . ASP . rr_1eii 1 5 . GLN . rr_1eii 1 6 . ASN . rr_1eii 1 7 . GLY . rr_1eii 1 8 . THR . rr_1eii 1 9 . TRP . rr_1eii 1 10 . GLU . rr_1eii 1 11 . MET . rr_1eii 1 12 . GLU . rr_1eii 1 13 . SER . rr_1eii 1 14 . ASN . rr_1eii 1 15 . GLU . rr_1eii 1 16 . ASN . rr_1eii 1 17 . PHE . rr_1eii 1 18 . GLU . rr_1eii 1 19 . GLY . rr_1eii 1 20 . TYR . rr_1eii 1 21 . MET . rr_1eii 1 22 . LYS . rr_1eii 1 23 . ALA . rr_1eii 1 24 . LEU . rr_1eii 1 25 . ASP . rr_1eii 1 26 . ILE . rr_1eii 1 27 . ASP . rr_1eii 1 28 . PHE . rr_1eii 1 29 . ALA . rr_1eii 1 30 . THR . rr_1eii 1 31 . ARG . rr_1eii 1 32 . LYS . rr_1eii 1 33 . ILE . rr_1eii 1 34 . ALA . rr_1eii 1 35 . VAL . rr_1eii 1 36 . ARG . rr_1eii 1 37 . LEU . rr_1eii 1 38 . THR . rr_1eii 1 39 . GLN . rr_1eii 1 40 . THR . rr_1eii 1 41 . LYS . rr_1eii 1 42 . ILE . rr_1eii 1 43 . ILE . rr_1eii 1 44 . VAL . rr_1eii 1 45 . GLN . rr_1eii 1 46 . ASP . rr_1eii 1 47 . GLY . rr_1eii 1 48 . ASP . rr_1eii 1 49 . ASN . rr_1eii 1 50 . PHE . rr_1eii 1 51 . LYS . rr_1eii 1 52 . THR . rr_1eii 1 53 . LYS . rr_1eii 1 54 . THR . rr_1eii 1 55 . ASN . rr_1eii 1 56 . SER . rr_1eii 1 57 . THR . rr_1eii 1 58 . PHE . rr_1eii 1 59 . ARG . rr_1eii 1 60 . ASN . rr_1eii 1 61 . TYR . rr_1eii 1 62 . ASP . rr_1eii 1 63 . LEU . rr_1eii 1 64 . ASP . rr_1eii 1 65 . PHE . rr_1eii 1 66 . THR . rr_1eii 1 67 . VAL . rr_1eii 1 68 . GLY . rr_1eii 1 69 . VAL . rr_1eii 1 70 . GLU . rr_1eii 1 71 . PHE . rr_1eii 1 72 . ASP . rr_1eii 1 73 . GLU . rr_1eii 1 74 . HIS . rr_1eii 1 75 . THR . rr_1eii 1 76 . LYS . rr_1eii 1 77 . GLY . rr_1eii 1 78 . LEU . rr_1eii 1 79 . ASP . rr_1eii 1 80 . GLY . rr_1eii 1 81 . ARG . rr_1eii 1 82 . ASN . rr_1eii 1 83 . VAL . rr_1eii 1 84 . LYS . rr_1eii 1 85 . THR . rr_1eii 1 86 . LEU . rr_1eii 1 87 . VAL . rr_1eii 1 88 . THR . rr_1eii 1 89 . TRP . rr_1eii 1 90 . GLU . rr_1eii 1 91 . GLY . rr_1eii 1 92 . ASN . rr_1eii 1 93 . THR . rr_1eii 1 94 . LEU . rr_1eii 1 95 . VAL . rr_1eii 1 96 . CYS . rr_1eii 1 97 . VAL . rr_1eii 1 98 . GLN . rr_1eii 1 99 . LYS . rr_1eii 1 100 . GLY . rr_1eii 1 101 . GLU . rr_1eii 1 102 . LYS . rr_1eii 1 103 . GLU . rr_1eii 1 104 . ASN . rr_1eii 1 105 . ARG . rr_1eii 1 106 . GLY . rr_1eii 1 107 . TRP . rr_1eii 1 108 . LYS . rr_1eii 1 109 . GLN . rr_1eii 1 110 . TRP . rr_1eii 1 111 . VAL . rr_1eii 1 112 . GLU . rr_1eii 1 113 . GLY . rr_1eii 1 114 . ASP . rr_1eii 1 115 . LYS . rr_1eii 1 116 . LEU . rr_1eii 1 117 . TYR . rr_1eii 1 118 . LEU . rr_1eii 1 119 . GLU . rr_1eii 1 120 . LEU . rr_1eii 1 121 . THR . rr_1eii 1 122 . CYS . rr_1eii 1 123 . GLY . rr_1eii 1 124 . ASP . rr_1eii 1 125 . GLN . rr_1eii 1 126 . VAL . rr_1eii 1 127 . CYS . rr_1eii 1 128 . ARG . rr_1eii 1 129 . GLN . rr_1eii 1 130 . VAL . rr_1eii 1 131 . PHE . rr_1eii 1 132 . LYS . rr_1eii 1 133 . LYS . rr_1eii 1 134 . LYS . rr_1eii 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 . MET 1 1 rr_1eii 1 . THR 2 2 rr_1eii 1 . LYS 3 3 rr_1eii 1 . ASP 4 4 rr_1eii 1 . GLN 5 5 rr_1eii 1 . ASN 6 6 rr_1eii 1 . GLY 7 7 rr_1eii 1 . THR 8 8 rr_1eii 1 . TRP 9 9 rr_1eii 1 . GLU 10 10 rr_1eii 1 . MET 11 11 rr_1eii 1 . GLU 12 12 rr_1eii 1 . SER 13 13 rr_1eii 1 . ASN 14 14 rr_1eii 1 . GLU 15 15 rr_1eii 1 . ASN 16 16 rr_1eii 1 . PHE 17 17 rr_1eii 1 . GLU 18 18 rr_1eii 1 . GLY 19 19 rr_1eii 1 . TYR 20 20 rr_1eii 1 . MET 21 21 rr_1eii 1 . LYS 22 22 rr_1eii 1 . ALA 23 23 rr_1eii 1 . LEU 24 24 rr_1eii 1 . ASP 25 25 rr_1eii 1 . ILE 26 26 rr_1eii 1 . ASP 27 27 rr_1eii 1 . PHE 28 28 rr_1eii 1 . ALA 29 29 rr_1eii 1 . THR 30 30 rr_1eii 1 . ARG 31 31 rr_1eii 1 . LYS 32 32 rr_1eii 1 . ILE 33 33 rr_1eii 1 . ALA 34 34 rr_1eii 1 . VAL 35 35 rr_1eii 1 . ARG 36 36 rr_1eii 1 . LEU 37 37 rr_1eii 1 . THR 38 38 rr_1eii 1 . GLN 39 39 rr_1eii 1 . THR 40 40 rr_1eii 1 . LYS 41 41 rr_1eii 1 . ILE 42 42 rr_1eii 1 . ILE 43 43 rr_1eii 1 . VAL 44 44 rr_1eii 1 . GLN 45 45 rr_1eii 1 . ASP 46 46 rr_1eii 1 . GLY 47 47 rr_1eii 1 . ASP 48 48 rr_1eii 1 . ASN 49 49 rr_1eii 1 . PHE 50 50 rr_1eii 1 . LYS 51 51 rr_1eii 1 . THR 52 52 rr_1eii 1 . LYS 53 53 rr_1eii 1 . THR 54 54 rr_1eii 1 . ASN 55 55 rr_1eii 1 . SER 56 56 rr_1eii 1 . THR 57 57 rr_1eii 1 . PHE 58 58 rr_1eii 1 . ARG 59 59 rr_1eii 1 . ASN 60 60 rr_1eii 1 . TYR 61 61 rr_1eii 1 . ASP 62 62 rr_1eii 1 . LEU 63 63 rr_1eii 1 . ASP 64 64 rr_1eii 1 . PHE 65 65 rr_1eii 1 . THR 66 66 rr_1eii 1 . VAL 67 67 rr_1eii 1 . GLY 68 68 rr_1eii 1 . VAL 69 69 rr_1eii 1 . GLU 70 70 rr_1eii 1 . PHE 71 71 rr_1eii 1 . ASP 72 72 rr_1eii 1 . GLU 73 73 rr_1eii 1 . HIS 74 74 rr_1eii 1 . THR 75 75 rr_1eii 1 . LYS 76 76 rr_1eii 1 . GLY 77 77 rr_1eii 1 . LEU 78 78 rr_1eii 1 . ASP 79 79 rr_1eii 1 . GLY 80 80 rr_1eii 1 . ARG 81 81 rr_1eii 1 . ASN 82 82 rr_1eii 1 . VAL 83 83 rr_1eii 1 . LYS 84 84 rr_1eii 1 . THR 85 85 rr_1eii 1 . LEU 86 86 rr_1eii 1 . VAL 87 87 rr_1eii 1 . THR 88 88 rr_1eii 1 . TRP 89 89 rr_1eii 1 . GLU 90 90 rr_1eii 1 . GLY 91 91 rr_1eii 1 . ASN 92 92 rr_1eii 1 . THR 93 93 rr_1eii 1 . LEU 94 94 rr_1eii 1 . VAL 95 95 rr_1eii 1 . CYS 96 96 rr_1eii 1 . VAL 97 97 rr_1eii 1 . GLN 98 98 rr_1eii 1 . LYS 99 99 rr_1eii 1 . GLY 100 100 rr_1eii 1 . GLU 101 101 rr_1eii 1 . LYS 102 102 rr_1eii 1 . GLU 103 103 rr_1eii 1 . ASN 104 104 rr_1eii 1 . ARG 105 105 rr_1eii 1 . GLY 106 106 rr_1eii 1 . TRP 107 107 rr_1eii 1 . LYS 108 108 rr_1eii 1 . GLN 109 109 rr_1eii 1 . TRP 110 110 rr_1eii 1 . VAL 111 111 rr_1eii 1 . GLU 112 112 rr_1eii 1 . GLY 113 113 rr_1eii 1 . ASP 114 114 rr_1eii 1 . LYS 115 115 rr_1eii 1 . LEU 116 116 rr_1eii 1 . TYR 117 117 rr_1eii 1 . LEU 118 118 rr_1eii 1 . GLU 119 119 rr_1eii 1 . LEU 120 120 rr_1eii 1 . THR 121 121 rr_1eii 1 . CYS 122 122 rr_1eii 1 . GLY 123 123 rr_1eii 1 . ASP 124 124 rr_1eii 1 . GLN 125 125 rr_1eii 1 . VAL 126 126 rr_1eii 1 . CYS 127 127 rr_1eii 1 . ARG 128 128 rr_1eii 1 . GLN 129 129 rr_1eii 1 . VAL 130 130 rr_1eii 1 . PHE 131 131 rr_1eii 1 . LYS 132 132 rr_1eii 1 . LYS 133 133 rr_1eii 1 . LYS 134 134 rr_1eii 1 stop_ save_ save_RETINOL _Entity.Sf_category entity _Entity.Sf_framecode RETINOL _Entity.Entry_ID rr_1eii _Entity.ID 2 _Entity.Name RETINOL _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 RTL _Entity.Nonpolymer_comp_label $chem_comp_RTL _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 . RTL . rr_1eii 2 stop_ save_ save_chem_comp_RTL _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_RTL _Chem_comp.Entry_ID rr_1eii _Chem_comp.ID RTL _Chem_comp.Name RETINOL _Chem_comp.Type non-polymer _Chem_comp.PDB_code RTL _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic no _Chem_comp.Aromatic no _Chem_comp.Formula "C20 H30 O" _Chem_comp.Formula_weight 286.4564 save_ save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_1eii _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 25 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_1eii _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 1eii.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1eii 1 1 1eii.mr . . unknown 2 distance NOE simple 0 rr_1eii 1 1 1eii.mr . . unknown 3 sequence "Not applicable" "Not applicable" 0 rr_1eii 1 1 1eii.mr . . PDB 4 coordinate initial "Not applicable" 0 rr_1eii 1 1 1eii.mr . . n/a 5 comment "Not applicable" "Not applicable" 0 rr_1eii 1 1 1eii.mr . . TINKER 6 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1eii 1 1 1eii.mr . . TINKER 7 distance NOE simple 0 rr_1eii 1 1 1eii.mr . . "MR format" 8 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1eii 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_1eii _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 TRANSPORT PROTEIN 25-FEB-00 1EII *TITLE NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: CELLULAR RETINOL-BINDING PROTEIN II; *COMPND 3 CHAIN: A; *COMPND 4 SYNONYM: CRBP-II; *COMPND 5 ENGINEERED: YES *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; *SOURCE 3 ORGANISM_COMMON: RAT; *SOURCE 4 CELL: SMALL INTESTINAL ENTEROCYTE; *SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; *SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; *SOURCE 7 EXPRESSION_SYSTEM_COMMON: BACTERIA; *SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM101; *SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PMON-CRBP II *KEYWDS PROTEIN-LIGAND COMPLEX, BETA BARREL, HELIX-TURN-HELIX *EXPDTA NMR, 25 STRUCTURES *AUTHOR J.LU, C.L.LIN, C.TANG, J.W.PONDER, J.L.KAO, D.P.CISTOLA, *AUTHOR 2 E.LI *REVDAT 1 09-AUG-00 1EII 0 # THIS FILE CONTAINS SIX SEPARATE FILES IN THE FOLLOWING ORDER: # 1. holo-crbpii.noe -- # RAW DISTANCE RESTRAINT LIST IN NMRCOMPASS VERSION 2.6 # FORMAT # 2. holo-crbpii.input -- # INPUT VALUES FOR RUNNING DISTGEOM # 3. holo-crbpii.seq -- # AMINO ACID SEQUENCE OF RAT CRBP II # 4. holo-crbpii.pdb -- # INITIAL STRUCTURE COORDINATES IN PDB FORMAT # 5. holo-crbpii.xyz -- # INITIAL STRUCTURE COORDINATES IN TINKER FORMAT # 6. holo-crbpii.key -- # COMPLETE DISTANCE AND DIHEDRAL ANGLE RESTRAINT LIST IN # TINKER FORMAT # ONLY THE LAST FIVE FILES WILL BE NEEDED IN ORDER TO REPRODUCE # THE FINAL STRUCTURE ENSEMBLE. ; 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_1eii _Org_constr_file_comment.ID 2 _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 ; ################### # holo-crbpii.key # ################### parameters /usr/local/tinker/params/protein trial-distance pairwise 5 trial-distribution 0.61 ; save_