data_wwPDB_remediated_restraints_file_for_PDB_entry_1cdn # This wwPDB archive file contains, for PDB entry 1cdn: # # - 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_1cdn _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1cdn" _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 1cdn" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1cdn _Assembly.ID 1 _Assembly.Name 1cdn _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 8584.6421 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 "CALBINDIN D9K" 1 $CALBINDIN_D9K A . no . . . . . . rr_1cdn 1 stop_ save_ save_CALBINDIN_D9K _Entity.Sf_category entity _Entity.Sf_framecode CALBINDIN_D9K _Entity.Entry_ID rr_1cdn _Entity.ID 1 _Entity.Name CALBINDIN_D9K _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; MKSPEELKGIFEKYAAKEGD PNQLSKEELKLLLQTEFPSL LKGGSTLDELFEELDKNGDG EVSFEEFQVLVKKISQ ; _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 76 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 8584.6421 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_1cdn 1 2 . LYS . rr_1cdn 1 3 . SER . rr_1cdn 1 4 . PRO . rr_1cdn 1 5 . GLU . rr_1cdn 1 6 . GLU . rr_1cdn 1 7 . LEU . rr_1cdn 1 8 . LYS . rr_1cdn 1 9 . GLY . rr_1cdn 1 10 . ILE . rr_1cdn 1 11 . PHE . rr_1cdn 1 12 . GLU . rr_1cdn 1 13 . LYS . rr_1cdn 1 14 . TYR . rr_1cdn 1 15 . ALA . rr_1cdn 1 16 . ALA . rr_1cdn 1 17 . LYS . rr_1cdn 1 18 . GLU . rr_1cdn 1 19 . GLY . rr_1cdn 1 20 . ASP . rr_1cdn 1 21 . PRO . rr_1cdn 1 22 . ASN . rr_1cdn 1 23 . GLN . rr_1cdn 1 24 . LEU . rr_1cdn 1 25 . SER . rr_1cdn 1 26 . LYS . rr_1cdn 1 27 . GLU . rr_1cdn 1 28 . GLU . rr_1cdn 1 29 . LEU . rr_1cdn 1 30 . LYS . rr_1cdn 1 31 . LEU . rr_1cdn 1 32 . LEU . rr_1cdn 1 33 . LEU . rr_1cdn 1 34 . GLN . rr_1cdn 1 35 . THR . rr_1cdn 1 36 . GLU . rr_1cdn 1 37 . PHE . rr_1cdn 1 38 . PRO . rr_1cdn 1 39 . SER . rr_1cdn 1 40 . LEU . rr_1cdn 1 41 . LEU . rr_1cdn 1 42 . LYS . rr_1cdn 1 43 . GLY . rr_1cdn 1 44 . GLY . rr_1cdn 1 45 . SER . rr_1cdn 1 46 . THR . rr_1cdn 1 47 . LEU . rr_1cdn 1 48 . ASP . rr_1cdn 1 49 . GLU . rr_1cdn 1 50 . LEU . rr_1cdn 1 51 . PHE . rr_1cdn 1 52 . GLU . rr_1cdn 1 53 . GLU . rr_1cdn 1 54 . LEU . rr_1cdn 1 55 . ASP . rr_1cdn 1 56 . LYS . rr_1cdn 1 57 . ASN . rr_1cdn 1 58 . GLY . rr_1cdn 1 59 . ASP . rr_1cdn 1 60 . GLY . rr_1cdn 1 61 . GLU . rr_1cdn 1 62 . VAL . rr_1cdn 1 63 . SER . rr_1cdn 1 64 . PHE . rr_1cdn 1 65 . GLU . rr_1cdn 1 66 . GLU . rr_1cdn 1 67 . PHE . rr_1cdn 1 68 . GLN . rr_1cdn 1 69 . VAL . rr_1cdn 1 70 . LEU . rr_1cdn 1 71 . VAL . rr_1cdn 1 72 . LYS . rr_1cdn 1 73 . LYS . rr_1cdn 1 74 . ILE . rr_1cdn 1 75 . SER . rr_1cdn 1 76 . GLN . rr_1cdn 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_1cdn 1 . LYS 2 2 rr_1cdn 1 . SER 3 3 rr_1cdn 1 . PRO 4 4 rr_1cdn 1 . GLU 5 5 rr_1cdn 1 . GLU 6 6 rr_1cdn 1 . LEU 7 7 rr_1cdn 1 . LYS 8 8 rr_1cdn 1 . GLY 9 9 rr_1cdn 1 . ILE 10 10 rr_1cdn 1 . PHE 11 11 rr_1cdn 1 . GLU 12 12 rr_1cdn 1 . LYS 13 13 rr_1cdn 1 . TYR 14 14 rr_1cdn 1 . ALA 15 15 rr_1cdn 1 . ALA 16 16 rr_1cdn 1 . LYS 17 17 rr_1cdn 1 . GLU 18 18 rr_1cdn 1 . GLY 19 19 rr_1cdn 1 . ASP 20 20 rr_1cdn 1 . PRO 21 21 rr_1cdn 1 . ASN 22 22 rr_1cdn 1 . GLN 23 23 rr_1cdn 1 . LEU 24 24 rr_1cdn 1 . SER 25 25 rr_1cdn 1 . LYS 26 26 rr_1cdn 1 . GLU 27 27 rr_1cdn 1 . GLU 28 28 rr_1cdn 1 . LEU 29 29 rr_1cdn 1 . LYS 30 30 rr_1cdn 1 . LEU 31 31 rr_1cdn 1 . LEU 32 32 rr_1cdn 1 . LEU 33 33 rr_1cdn 1 . GLN 34 34 rr_1cdn 1 . THR 35 35 rr_1cdn 1 . GLU 36 36 rr_1cdn 1 . PHE 37 37 rr_1cdn 1 . PRO 38 38 rr_1cdn 1 . SER 39 39 rr_1cdn 1 . LEU 40 40 rr_1cdn 1 . LEU 41 41 rr_1cdn 1 . LYS 42 42 rr_1cdn 1 . GLY 43 43 rr_1cdn 1 . GLY 44 44 rr_1cdn 1 . SER 45 45 rr_1cdn 1 . THR 46 46 rr_1cdn 1 . LEU 47 47 rr_1cdn 1 . ASP 48 48 rr_1cdn 1 . GLU 49 49 rr_1cdn 1 . LEU 50 50 rr_1cdn 1 . PHE 51 51 rr_1cdn 1 . GLU 52 52 rr_1cdn 1 . GLU 53 53 rr_1cdn 1 . LEU 54 54 rr_1cdn 1 . ASP 55 55 rr_1cdn 1 . LYS 56 56 rr_1cdn 1 . ASN 57 57 rr_1cdn 1 . GLY 58 58 rr_1cdn 1 . ASP 59 59 rr_1cdn 1 . GLY 60 60 rr_1cdn 1 . GLU 61 61 rr_1cdn 1 . VAL 62 62 rr_1cdn 1 . SER 63 63 rr_1cdn 1 . PHE 64 64 rr_1cdn 1 . GLU 65 65 rr_1cdn 1 . GLU 66 66 rr_1cdn 1 . PHE 67 67 rr_1cdn 1 . GLN 68 68 rr_1cdn 1 . VAL 69 69 rr_1cdn 1 . LEU 70 70 rr_1cdn 1 . VAL 71 71 rr_1cdn 1 . LYS 72 72 rr_1cdn 1 . LYS 73 73 rr_1cdn 1 . ILE 74 74 rr_1cdn 1 . SER 75 75 rr_1cdn 1 . GLN 76 76 rr_1cdn 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_1cdn _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 24 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_1cdn _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 1cdn.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1cdn 1 1 1cdn.mr . . "MR format" 2 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1cdn 1 1 1cdn.mr . . n/a 3 comment "Not applicable" "Not applicable" 0 rr_1cdn 1 1 1cdn.mr . . "MR format" 4 distance NOE simple 0 rr_1cdn 1 1 1cdn.mr . . "MR format" 5 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1cdn 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_1cdn _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 CALCIUM-BINDING PROTEIN 04-AUG-95 1CDN *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: CALBINDIN D9K; *COMPND 3 CHAIN: NULL; *COMPND 4 SYNONYM: INTESTINAL CALCIUM-BINDING PROTEIN, ICBP, ICABP, *COMPND 5 CABP9K, S100D; *COMPND 6 ENGINEERED: YES; *COMPND 7 MUTATION: INS(MET 1), P43G; *COMPND 8 OTHER_DETAILS: BOVINE MINOR A FORM, CADMIUM-HALF-SATURATED, *COMPND 9 CADMIUM ION IS BOUND IN C-TERMINAL SITE *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; *SOURCE 3 ORGANISM_COMMON: BOVINE; *SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; *SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PICB1; *SOURCE 6 EXPRESSION_SYSTEM_GENE: ICABP *KEYWDS EF-HAND *EXPDTA NMR, 24 STRUCTURES *AUTHOR M.AKKE,S.FORSEN,W.J.CHAZIN *REVDAT 1 14-NOV-95 1CDN 0 HEADER CALCIUM-BINDING PROTEIN COMPND CALBINDIN D9K (BOVINE MINOR A FORM, CADMIUM-HALF-SATURATED, COMPND 2 CADMIUM ION IS BOUND IN THE C-TERMINAL SITE) COMPND 3 (INTESTINAL CALCIUM BINDING PROTEIN, ICBP, ICABP, CABP9K, COMPND 4 S100D) MUTANT WITH N-TERMINAL MET, PRO 43 REPLACED BY GLY COMPND 5 (INS(MET 0),P43G) (NMR, 24 STRUCTURES) SOURCE CALBINDIN D9K: BOVINE (BOS TAURUS) SOURCE 2 EXPRESSION SYSTEM: (ESCHERICHIA COLI) SOURCE 3 PLASMID: PICB1 SOURCE 4 GENE: ICABP EXPDTA NMR AUTHOR M.AKKE,W.J.CHAZIN REVDAT REMARK 2 REMARK 2 HYDROGEN ATOMS IN THIS RESTRAINT SET HAVE BEEN GIVEN REMARK 2 NAMES CONSISTENT WITH THE RECOMMENDATIONS OF THE IUPAC-IUB REMARK 2 COMMISSION ON BIOCHEMICAL NOMENCLATURE (SEE, E.G., J.MOL. REMARK 2 BIOL. 52, 1 (1970)), AND WHERE POSSIBLE, ARE CONSISTENT WITH REMARK 2 HYDROGEN ATOM NAMES IN THE CORRESPONDING PDB COORDINATE ENTRY REMARK 2 FOR (CD2+)1 CALBINDIN D9K. REMARK 2 REMARK 3 REMARK 3 (CD2+)1 CALBINDIN D9K NMR RESTRAINTS USED IN STRUCTURE REMARK 3 DETERMINATION. COMPLETE LIST OF NOE AND DIHEDRAL ANGLE REMARK 3 RESTRAINTS. REMARK 3 REMARK 3 DIHEDRAL ANGLE RESTRAINTS-- REMARK 3 DIHEDRAL ANGLE RESTRAINTS ARE DERIVED FROM EXPERIMENTALLY REMARK 3 MEASURED 3JHNA, 3JAB AND 3JNHB COUPLING CONSTANTS IN REMARK 3 ADDITION TO NOES INVOLVING NH, CA, AND, CB PROTONS. REMARK 3 CHI-2 DIHEDRAL ANGE RESTRAINTS WERE INFERRED BY COMPARISON REMARK 3 OF THE EXPERIMENTAL AND THEORETICAL RELATIVE NOE REMARK 3 INTENSITIES FOR THE INTRA-RESIDUE HB-HD CROSS-PEAKS, AS REMARK 3 DESCRIBED IN THE PAPER CITED IN THE JRNL RECORD OF THE REMARK 3 COORDINATE FILE. REMARK 3 IN TOTAL THERE ARE 40 PHI, 27 CHI1 AND 4 CHI2 CONSTRAINTS. REMARK 3 REMARK 3 TABLE OF DIHEDRAL ANGLE RESTRAINT BOUNDS REMARK 3 ------------------------------------------------------- ; 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_1cdn _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 ; REMARK 3 NOE DERIVED DISTANCE UPPER BOUND RESTRAINTS-- REMARK 3 THE COMPLETE SET OF DISTANCE UPPER-BOUNDS DERIVED FROM NOES REMARK 3 FOR (CD2+)1 CALBINDIN D9K ARE GIVEN BELOW. REMARK 3 THESE ARE THE "RAW" CONSTRAINTS WITHOUT ANY CORRECTIONS REMARK 3 APPLIED TO BOUNDS INVOLVING NON-STEREO-SPECIFICALLY REMARK 3 ASSIGNED PROTONS. REMARK 3 THE BOUNDS ARE DERIVED DIFFERENTLY FOR *DISGEO* AND *AMBER REMARK 3 CALCULATIONS, DEPENDING ON THE TREATMENT OF NON-STEREO- REMARK 3 SPECIFICALLY ASSIGNED PROTONS. REMARK 3 REMARK 3 RESTRAINTS EXACTLY AS WOULD BE USED FOR *DISGEO* AND REMARK 3 *AMBER* CALCULATIONS MAY BE OBTAINED VIA EMAIL FROM THE REMARK 3 AUTHORS: CHAZIN@SCRIPPS.EDU REMARK 3 REMARK 3 *DISGEO*- A MIXED PSEUDO-ATOM/ALL-ATOM REPRESENTATION WAS REMARK 3 USED IN WHICH ALL ALPHA, BETA, GAMMA, AND DELTA REMARK 3 METHYLENE PROTONS ARE REPRESENTED BY EITHER PROTON OR REMARK 3 PSEUDO-ATOM POINTS. REMARK 3 REMARK 3 *AMBER*- ALL-ATOM STRUCTURES WERE USED. (R**-6) DISTANCE REMARK 3 WEIGHTING WAS USED FOR ALL NON-STEREO-SPECIFICALLY REMARK 3 ASSIGNED DIASTEREOTOPIC PROTONS, INCLUDING METHYL REMARK 3 GROUPS. AMBIGUOUS NOE RESTRAINTS (CHEMICAL-SHIFT REMARK 3 DEGENERATE VAL AND LEU METHYLS, OR WHEN ONLY ONE OF REMARK 3 TWO NON-STEREO-ASSIGNED METHYLS EXHIBITS AN NOE), REMARK 3 ARE REFERRED TO COMMON CB OR CG ATOMS, RESPECTIVELY. REMARK 3 REMARK 3 PSEUDOATOM NAMES ARE USED FOR DIASTEREOTOPIC PROTONS, REMARK 3 FOR WHICH STEREOSPECIFIC ASSIGNMENTS COULD NOT BE MADE, REMARK 3 AS INDICATED BY A LEADING "Q". METHYL AND METHYLENE REMARK 3 GROUP PROTONS ARE INDICATED BY "M" AND "H", RESPECTIVELY. REMARK 3 REMARK 3 THE FOLLOWING LIST CONTAINS REMARK 3 203 INTRARESIDUE NOES REMARK 3 237 SEQUENTIAL NOES REMARK 3 240 MEDIUM-RANGE NOES REMARK 3 265 LONG-RANGE NOES REMARK 3 945 TOTAL NOES REMARK 3 REMARK 3 TABLE OF DISTANCE RESTRAINT UPPER BOUNDS (IN ANGSTROMS) REMARK 3 ATOM 1 ATOM 2 DISTBND REMARK 3 ----------------------------------------------- ; save_