data_wwPDB_remediated_restraints_file_for_PDB_entry_1cb1 # This wwPDB archive file contains, for PDB entry 1cb1: # # - 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_1cb1 _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1cb1" _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 1cb1" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1cb1 _Assembly.ID 1 _Assembly.Name 1cb1 _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 8793.8574 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_1cb1 1 stop_ save_ save_CALBINDIN_D9K _Entity.Sf_category entity _Entity.Sf_framecode CALBINDIN_D9K _Entity.Entry_ID rr_1cb1 _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 ; SAQKSPAELKSIFEKYAAKE GDPNQLSKEELKQLIQAEFP SLLKGPRTLDDLFQELDKNG DGEVSFEEFQVLVKKISQ ; _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 78 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 8793.8574 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 . SER . rr_1cb1 1 2 . ALA . rr_1cb1 1 3 . GLN . rr_1cb1 1 4 . LYS . rr_1cb1 1 5 . SER . rr_1cb1 1 6 . PRO . rr_1cb1 1 7 . ALA . rr_1cb1 1 8 . GLU . rr_1cb1 1 9 . LEU . rr_1cb1 1 10 . LYS . rr_1cb1 1 11 . SER . rr_1cb1 1 12 . ILE . rr_1cb1 1 13 . PHE . rr_1cb1 1 14 . GLU . rr_1cb1 1 15 . LYS . rr_1cb1 1 16 . TYR . rr_1cb1 1 17 . ALA . rr_1cb1 1 18 . ALA . rr_1cb1 1 19 . LYS . rr_1cb1 1 20 . GLU . rr_1cb1 1 21 . GLY . rr_1cb1 1 22 . ASP . rr_1cb1 1 23 . PRO . rr_1cb1 1 24 . ASN . rr_1cb1 1 25 . GLN . rr_1cb1 1 26 . LEU . rr_1cb1 1 27 . SER . rr_1cb1 1 28 . LYS . rr_1cb1 1 29 . GLU . rr_1cb1 1 30 . GLU . rr_1cb1 1 31 . LEU . rr_1cb1 1 32 . LYS . rr_1cb1 1 33 . GLN . rr_1cb1 1 34 . LEU . rr_1cb1 1 35 . ILE . rr_1cb1 1 36 . GLN . rr_1cb1 1 37 . ALA . rr_1cb1 1 38 . GLU . rr_1cb1 1 39 . PHE . rr_1cb1 1 40 . PRO . rr_1cb1 1 41 . SER . rr_1cb1 1 42 . LEU . rr_1cb1 1 43 . LEU . rr_1cb1 1 44 . LYS . rr_1cb1 1 45 . GLY . rr_1cb1 1 46 . PRO . rr_1cb1 1 47 . ARG . rr_1cb1 1 48 . THR . rr_1cb1 1 49 . LEU . rr_1cb1 1 50 . ASP . rr_1cb1 1 51 . ASP . rr_1cb1 1 52 . LEU . rr_1cb1 1 53 . PHE . rr_1cb1 1 54 . GLN . rr_1cb1 1 55 . GLU . rr_1cb1 1 56 . LEU . rr_1cb1 1 57 . ASP . rr_1cb1 1 58 . LYS . rr_1cb1 1 59 . ASN . rr_1cb1 1 60 . GLY . rr_1cb1 1 61 . ASP . rr_1cb1 1 62 . GLY . rr_1cb1 1 63 . GLU . rr_1cb1 1 64 . VAL . rr_1cb1 1 65 . SER . rr_1cb1 1 66 . PHE . rr_1cb1 1 67 . GLU . rr_1cb1 1 68 . GLU . rr_1cb1 1 69 . PHE . rr_1cb1 1 70 . GLN . rr_1cb1 1 71 . VAL . rr_1cb1 1 72 . LEU . rr_1cb1 1 73 . VAL . rr_1cb1 1 74 . LYS . rr_1cb1 1 75 . LYS . rr_1cb1 1 76 . ILE . rr_1cb1 1 77 . SER . rr_1cb1 1 78 . GLN . rr_1cb1 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 . SER 1 1 rr_1cb1 1 . ALA 2 2 rr_1cb1 1 . GLN 3 3 rr_1cb1 1 . LYS 4 4 rr_1cb1 1 . SER 5 5 rr_1cb1 1 . PRO 6 6 rr_1cb1 1 . ALA 7 7 rr_1cb1 1 . GLU 8 8 rr_1cb1 1 . LEU 9 9 rr_1cb1 1 . LYS 10 10 rr_1cb1 1 . SER 11 11 rr_1cb1 1 . ILE 12 12 rr_1cb1 1 . PHE 13 13 rr_1cb1 1 . GLU 14 14 rr_1cb1 1 . LYS 15 15 rr_1cb1 1 . TYR 16 16 rr_1cb1 1 . ALA 17 17 rr_1cb1 1 . ALA 18 18 rr_1cb1 1 . LYS 19 19 rr_1cb1 1 . GLU 20 20 rr_1cb1 1 . GLY 21 21 rr_1cb1 1 . ASP 22 22 rr_1cb1 1 . PRO 23 23 rr_1cb1 1 . ASN 24 24 rr_1cb1 1 . GLN 25 25 rr_1cb1 1 . LEU 26 26 rr_1cb1 1 . SER 27 27 rr_1cb1 1 . LYS 28 28 rr_1cb1 1 . GLU 29 29 rr_1cb1 1 . GLU 30 30 rr_1cb1 1 . LEU 31 31 rr_1cb1 1 . LYS 32 32 rr_1cb1 1 . GLN 33 33 rr_1cb1 1 . LEU 34 34 rr_1cb1 1 . ILE 35 35 rr_1cb1 1 . GLN 36 36 rr_1cb1 1 . ALA 37 37 rr_1cb1 1 . GLU 38 38 rr_1cb1 1 . PHE 39 39 rr_1cb1 1 . PRO 40 40 rr_1cb1 1 . SER 41 41 rr_1cb1 1 . LEU 42 42 rr_1cb1 1 . LEU 43 43 rr_1cb1 1 . LYS 44 44 rr_1cb1 1 . GLY 45 45 rr_1cb1 1 . PRO 46 46 rr_1cb1 1 . ARG 47 47 rr_1cb1 1 . THR 48 48 rr_1cb1 1 . LEU 49 49 rr_1cb1 1 . ASP 50 50 rr_1cb1 1 . ASP 51 51 rr_1cb1 1 . LEU 52 52 rr_1cb1 1 . PHE 53 53 rr_1cb1 1 . GLN 54 54 rr_1cb1 1 . GLU 55 55 rr_1cb1 1 . LEU 56 56 rr_1cb1 1 . ASP 57 57 rr_1cb1 1 . LYS 58 58 rr_1cb1 1 . ASN 59 59 rr_1cb1 1 . GLY 60 60 rr_1cb1 1 . ASP 61 61 rr_1cb1 1 . GLY 62 62 rr_1cb1 1 . GLU 63 63 rr_1cb1 1 . VAL 64 64 rr_1cb1 1 . SER 65 65 rr_1cb1 1 . PHE 66 66 rr_1cb1 1 . GLU 67 67 rr_1cb1 1 . GLU 68 68 rr_1cb1 1 . PHE 69 69 rr_1cb1 1 . GLN 70 70 rr_1cb1 1 . VAL 71 71 rr_1cb1 1 . LEU 72 72 rr_1cb1 1 . VAL 73 73 rr_1cb1 1 . LYS 74 74 rr_1cb1 1 . LYS 75 75 rr_1cb1 1 . ILE 76 76 rr_1cb1 1 . SER 77 77 rr_1cb1 1 . GLN 78 78 rr_1cb1 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_1cb1 _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 13 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_1cb1 _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 1cb1.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1cb1 1 1 1cb1.mr . . "MR format" 2 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1cb1 1 1 1cb1.mr . . n/a 3 comment "Not applicable" "Not applicable" 0 rr_1cb1 1 1 1cb1.mr . . "MR format" 4 distance NOE simple 0 rr_1cb1 1 1 1cb1.mr . . "MR format" 5 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1cb1 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_1cb1 _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 13-DEC-91 1CB1 *COMPND CALBINDIN D9K (INTACT FORM) (NMR, 13 STRUCTURES) *SOURCE PORCINE (SUS SCROFA) INTESTINES *AUTHOR M.AKKE,T.DRAKENBERG,W.J.CHAZIN *REVDAT 1 31-OCT-93 1CB1 0 REMARK 3 REMARK 3 THE STRUCTURES WERE CALCULATED USING METRIC MATRIX DISTANCE REMARK 3 GEOMETRY, FOLLOWED BY A RESTRAINED MOLECULAR DYNAMICS REMARK 3 ANNEALING CYCLE EMPLOYING THE FULL AMBER FORCE FIELD. REMARK 3 REMARK 3 PROGRAMS USED: REMARK 3 *DISGEO*-DISTANCE GEOMETRY: REMARK 3 HAVEL, T.F., & WUTHRICH, K. REMARK 3 (1984) BULL. MATH. BIOL. 46, 673. REMARK 3 HAVEL, T.F., & WUTHRICH, K. REMARK 3 (1985) J. MOL. BIOL. 182, 281. REMARK 3 *AMBER*-RESTRAINED MOLECULAR DYNAMICS ANNEALING PROTOCOL: REMARK 3 GIPPERT, G.P., YIP, P., WRIGHT, P.E., & CASE, D.A. REMARK 3 (1990) BIOCHEM.PHARM. 40, 15 REMARK 4 REMARK 4 THESE COORDINATES WERE GENERATED FROM SOLUTION /NMR$ DATA. REMARK 4 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT *CRYST1* AND REMARK 4 *SCALE* RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 4 RECORDS ARE MEANINGLESS. REMARK 5 REMARK 5 DATA WERE COLLECTED AT PH 6.0 AND 300 K. REMARK 6 REMARK 6 PORCINE CALBINDIN D9K NMR-DERIVED CONSTRAINTS: REMARK 6 REMARK 6 A COMPLETE LIST OF EXPERIMENTAL CONSTRAINTS HAS BEEN REMARK 6 DEPOSITED WITH THE BROOKHAVEN PROTEIN DATA BANK. REMARK 6 A SUMMARY OF NMR CONSTRAINTS IS GIVEN BELOW. REMARK 6 REMARK 6 DISTANCE UPPER-BOUND CONSTRAINTS DERIVED FROM NOE DATA: REMARK 6 INTRA-RESIDUE 101 REMARK 6 INTER-RESIDUE 371 REMARK 6 TOTAL 472 REMARK 6 REMARK 6 HYDROGEN BOND CONSTRAINTS DERIVED FROM AMIDE PROTON REMARK 6 EXCHANGE AND NOE DATA: REMARK 6 10 HYDROGEN BONDS WERE CONSTRAINTED IN *DISGEO* REMARK 6 EACH HYDROGEN BOND IS IMPOSED AS TWO CONSTRAINTS: REMARK 6 NH-O = 1.8-2.0; N-O = 2.7-3.0 (ANGSTROM). REMARK 6 THUS, IN TOTAL 20 CONSTRAINTS WERE USED. REMARK 6 NO HYDROGEN BOND CONSTRAINTS WERE USED IN *AMBER* REMARK 6 REMARK 6 DIHEDRAL ANGLE CONSTRAINTS DERIVED FROM 3JHNA COUPLING REMARK 6 CONSTANTS MEASURED IN COSY SPECTRA: REMARK 6 27 RESIDUES -90 < PHI < -40 DEGREES (*DISGEO*) REMARK 6 9 RESIDUES -160 < PHI < -80 DEGREES (*DISGEO*) REMARK 6 2 RESIDUES -140 < PHI <-100 DEGREES (*DISGEO*) REMARK 6 27 RESIDUES -90 < PHI < 40 DEGREES (*AMBER*) REMARK 6 11 RESIDUES -160 < PHI < -80 DEGREES (*AMBER*) REMARK 7 REMARK 7 STRUCTURAL STATISTICS AND RESIDUAL VIOLATIONS: REMARK 7 REMARK 7 RMS DEVIATIONS OF COVALENT GEOMETRY FROM IDEALITY: REMARK 7 BOND LENGTHS: 0.006 ANGSTROMS REMARK 7 BOND ANGLES: 1.6 DEGREES REMARK 7 REMARK 7 AVERAGE MAXIMUM RESIDUAL CONSTRAINT VIOLATIONS: REMARK 7 DISTANCES: 0.33 ANGSTROMS REMARK 7 DIHEDRAL ANGLES: 9.3 DEGREES REMARK 7 REMARK 7 RESIDUAL CONSTRAINT AND TOTAL *AMBER* ENERGIES: REMARK 7 GIVEN FOR EACH MODEL. NOE CONSTRAINTS ARE MODELLED REMARK 7 AS A HALF-PARABOLA PENALTY FUNCTION WITH RESTORING REMARK 7 FORCE CONSTANT 32 KCAL/(MOL A**2). DIHEDRAL ANGLES REMARK 7 FALLING OUTSIDE THE PRESCRIBED LIMITS WERE PENALIZED REMARK 7 BY A FUNCTION OF THE FORM K(1-COS(W-W0)) WHERE W0 IS REMARK 7 THE ENDPOINT OF THE *ALLOWED* RANGE AND K=32 KCAL/MOL. REMARK 7 UNITS ARE KCAL/MOL. REMARK 7 REMARK 7 MODEL CONSTRAINT TOTAL REMARK 7 _________________________________________________ REMARK 7 1 23.6 -974.5 REMARK 7 2 22.1 -988.0 REMARK 7 3 21.7 -1017.0 REMARK 7 4 21.2 -1002.8 REMARK 7 5 21.6 -970.8 REMARK 7 6 18.4 -1009.8 REMARK 7 7 29.4 -996.2 REMARK 7 8 17.5 -1041.1 REMARK 7 9 19.1 -991.2 REMARK 7 10 34.9 -960.4 REMARK 7 11 17.1 -977.1 REMARK 7 12 31.2 -954.6 REMARK 7 13 25.0 -966.9 REMARK 7 14 22.6 -969.2 REMARK 7 REMARK 7 MODELS 1 THROUGH 14 CORRESPOND TO THE 14 "DG-RMD" REMARK 7 STRUCTURES REPORTED IN THE PAPER CITED ON *JRNL* REMARK 7 RECORDS ABOVE. REMARK 7 REMARK 7 MODELS 1 THROUGH 14 WERE BEST-FIT SUPERIMPOSED FOR THE REMARK 7 ATOMS SPECIFIED BELOW. UNITS ARE ANGSTROM. REMARK 7 REMARK 7 ALL RESIDUES. ALL HEAVY ATOMS: REMARK 7 PAIRWISE AVERAGE RMSD = 3.38 +/- 0.40 REMARK 7 AVERAGE RMSD FROM AVERAGE = 2.30 REMARK 7 ALL RESIDUES. CA, C, N ATOMS: REMARK 7 PAIRWISE AVERAGE RMSD = 2.80 +/- 0.46 REMARK 7 AVERAGE RMSD FROM AVERAGE = 1.91 REMARK 7 HELICES: REMARK 7 RESIDUES 7-19, 29-38, 49-57, 66-76. ATOMS CA, C, N: REMARK 7 PAIRWISE AVERAGE RMSD = 1.13 +/- 0.21 REMARK 7 AVERAGE RMSD FROM AVERAGE = 0.77 REMARK 7 REMARK 7 RESIDUE NUMBERING USED HERE (1 - 78) FOLLOWS SEQUENCE AS REMARK 7 LISTED IN *SEQRES* RECORDS BELOW. RESIDUE NUMBERING USED REMARK 7 IN THE PAPER CITED ON *JRNL* RECORDS ABOVE (-2 - 75) REMARK 7 FOLLOWED THE NUMBERING OF THE MINOR A FORM OF BOVINE REMARK 7 CALBINDIN D9K (FULLMER, C.S. & WASSERMAN, R.H. (1981) REMARK 7 J. BIOL. CHEM. 256, 5669). REMARK 8 REMARK 8 HYDROGEN ATOMS IN THIS ENTRY HAVE BEEN ASSIGNED NAMES REMARK 8 CONSISTENT WITH THE PROTEIN DATA BANK'S INTERPRETATION REMARK 8 OF THE RECOMMENDATIONS OF THE IUPAC-IUB COMMISSION ON REMARK 8 BIOCHEMICAL NOMENCLATURE (SEE, E.G., J. MOL. BIOL. 52, REMARK 8 1-17 (1970)). THUS, WHEN MORE THAN ONE HYDROGEN ATOM IS REMARK 8 BONDED TO A SINGLE NON-HYDROGEN ATOM, THE HYDROGEN ATOM REMARK 8 NUMBERING STARTS WITH 1, AND THE ATOM NUMBER DESIGNATION REMARK 8 IS GIVEN AS THE FIRST CHARACTER OF THE ATOM NAME RATHER REMARK 8 THAN THE LAST CHARACTER (E.G. H*BETA*1 IS DENOTED AS 1HB). SEQRES 1 78 SER ALA GLN LYS SER PRO ALA GLU LEU LYS SER ILE PHE SEQRES 2 78 GLU LYS TYR ALA ALA LYS GLU GLY ASP PRO ASN GLN LEU SEQRES 3 78 SER LYS GLU GLU LEU LYS GLN LEU ILE GLN ALA GLU PHE SEQRES 4 78 PRO SER LEU LEU LYS GLY PRO ARG THR LEU ASP ASP LEU SEQRES 5 78 PHE GLN GLU LEU ASP LYS ASN GLY ASP GLY GLU VAL SER SEQRES 6 78 PHE GLU GLU PHE GLN VAL LEU VAL LYS LYS ILE SER GLN CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 COMPND CALBINDIN D=9K= (PORCINE, INTACT FORM) (/NMR$, COMPND 2 14 STRUCTURES) SOURCE PORCINE (SUS $SCROFA) INTESTINE EXPDTA /NMR$ AUTHOR M.AKKE,T.DRAKENBERG,W.J.CHAZIN JRNL AUTH 1 M.AKKE,T.DRAKENBERG,W.J.CHAZIN JRNL TITL 1 THREE-DIMENSIONAL SOLUTION STRUCTURE OF JRNL TITL 2 CA==2+==-*LOADED PORCINE CALBINDIN D=9K= DETERMINED JRNL TITL 3 BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY JRNL REF BIOCHEMISTRY (ACCEPTED OCT 18, 1991) JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.DRAKENBERG,T.HOFMANN,W.J.CHAZIN REMARK 1 TITL 1 ==1==*H NMR STUDIES OF PORCINE CALBINDIN D=9K= IN REMARK 1 TITL 2 SOLUTION: SEQUENTIAL RESONANCE ASSIGNMENT, REMARK 1 TITL 3 SECONDARY STRUCTURE, AND GLOBAL FOLD REMARK 1 REF BIOCHEMISTRY V. 28 5946 1989 REMARK 1 REFN REMARK 2 REMARK 2 HYDROGEN ATOMS IN THIS CONSTRAINT 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 PORCINE CALBINDIN D9K. REMARK 2 REMARK 3 REMARK 3 PORCINE CALBINDIN D9K NMR RESTRAINTS USED IN STRUCTURE REMARK 3 DETERMINATION. COMPLETE LIST OF HYDROGEN-BOND, NOE AND REMARK 3 DIHEDRAL ANGLE CONSTRAINTS. REMARK 3 REMARK 3 REMARK 3 HYDROGEN BONDS CONSTRAINTS-- REMARK 3 10 HYDROGEN BOND DISTANCE CONSTRAINTS WERE USED FOR REMARK 3 *DISGEO* CALCULATIONS. NO HYDROGEN BOND CONSTRAINTS WERE REMARK 3 USED FOR *AMBER* RESTRAINED ENERGY MINIMIZATION OR REMARK 3 DYNAMICS CALCULATIONS. REMARK 3 REMARK 3 THE DISTANCE BOUNDS USED WERE: REMARK 3 (DONOR-ACCEPTOR, LOWER BOUND-UPPER BOUND) (ANGSTROM) REMARK 3 HN-O, 1.8-2.0 REMARK 3 N-O, 2.7-3.0 REMARK 3 REMARK 3 DONOR ACCEPTOR REMARK 3 ----------------------- REMARK 3 13 PHE 9 LEU REMARK 3 14 GLU 10 LYS REMARK 3 16 TYR 12 ILE REMARK 3 17 ALA 13 PHE REMARK 3 26 LEU 64 VAL REMARK 3 36 GLN 32 LYS REMARK 3 37 ALA 33 GLN REMARK 3 53 PHE 49 LEU REMARK 3 64 VAL 26 LEU REMARK 3 70 GLN 66 PHE REMARK 3 REMARK 3 REMARK 3 DIHEDRAL ANGLE CONSTRAINTS-- REMARK 3 PHI DIHEDRAL ANGLE CONSTRAINTS ARE DERIVED FROM MEASURED REMARK 3 3JHNA SCALAR COUPLING CONSTANTS. REMARK 3 REMARK 3 BOTH *DISGEO* AND *AMBER* CALCULATIONS UTILIZE THESE REMARK 3 DIHEDRAL ANGLE CONSTRAINTS, THOUGH FOR *DISGEO* THE REMARK 3 PHI CONSTRAINTS GIVEN BELOW AS -90 < PHI < 40 ARE GIVEN REMARK 3 THE MORE RESTRICTIVE RANGE -90 < PHI < -40, AND THE REMARK 3 RESIDUES WITH A "*" IN THE LAST FIELD OF THEIR RECORD REMARK 3 ARE GIVEN THE RANGE -140 < PHI < -100. REMARK 3 REMARK 3 DIHEDRAL CONSTRAINTS USED FOR FINAL STRUCTURE REFINEMENT 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_1cb1 _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 REMARK 3 REMARK 3 NOE DERIVED DISTANCE UPPER BOUND CONSTRAINTS-- REMARK 3 ALL EXPERIMENTALLY DERIVED NOE DISTANCE UPPER-BOUNDS USED REMARK 3 FOR PORCINE CALBINDIN D9K STRUCTURE CALCULATIONS ARE GIVEN REMARK 3 BELOW. DISTANCE CONSTRAINTS ARE DERIVED FROM THESE DISTANCE REMARK 3 BOUNDS DIFFERENTLY FOR *DISGEO* AND *AMBER CALCULATIONS. REMARK 3 CONSTRAINTS EXACTLY AS WOULD BE USED FOR *DISGEO* AND REMARK 3 *AMBER* CALCULATIONS MAY BE OBTAINED VIA EMAIL FROM THE REMARK 3 AUTHORS: AKKE@SCRIPPS.EDU OR 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 BOTH PROTON AND 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 CONSTRAINTS TO CHEMICAL-SHIFT REMARK 3 DEGENERATE VAL AND LEU METHYLS, OR WHERE ONLY ONE OF REMARK 3 THE TWO METHYLS IS OBSERVED TO EXHIBIT AN NOE, REMARK 3 ARE REFERRED TO COMMON CB OR CG ATOMS, RESPECTIVELY, REMARK 3 WITH A 2.2 ANGSTROMS CORRECTION. REMARK 3 REMARK 3 SINCE NO STEREO-SPECIFIC ASSIGNMENTS WERE MADE, REMARK 3 PSEUDOATOM NAMES ARE USED FOR ALL DIASTEREOTOPIC REMARK 3 PROTONS, INDICATED BY A LEADING "Q". REMARK 3 METHYL GROUPS ARE INDICATED BY "M", WHILE METHYLENE REMARK 3 PROTONS ARE INDICATED BY "H". REMARK 3 CHEMICAL SHIFTS ARE GIVEN IN PPM. REMARK 3 DISTANCE BOUNDS ARE GIVEN IN ANGSTROM. REMARK 3 REMARK 3 ATOM 1 ATOM 2 DIST CHEM CHEM REMARK 3 BND SHF1 SHF2 REMARK 3 ----------------------------------------------- ; save_