NMR Restraints Grid
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NMR Restraints Grid |
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Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | program | type | subtype |
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30284 |
1cb1   |
390 | cing | 2-parsed | STAR | entry | full |
data_1cb1_MR_file_constraints
save_Conversion_project
_Study_list.Sf_category study_list
_Study_list.Entry_ID parsed_1cb1
_Study_list.ID 1
loop_
_Study.ID
_Study.Name
_Study.Type
_Study.Details
_Study.Entry_ID
_Study.Study_list_ID
1 "Conversion project" NMR . parsed_1cb1 1
stop_
save_
save_entry_information
_Entry.Sf_category entry_information
_Entry.ID parsed_1cb1
_Entry.Title "Original constraint list(s)"
_Entry.Version_type original
_Entry.Submission_date .
_Entry.Accession_date .
_Entry.Last_release_date .
_Entry.Original_release_date .
_Entry.Origination .
_Entry.NMR_STAR_version 3.1
_Entry.Original_NMR_STAR_version .
_Entry.Experimental_method NMR
_Entry.Experimental_method_subtype .
loop_
_Related_entries.Database_name
_Related_entries.Database_accession_code
_Related_entries.Relationship
_Related_entries.Entry_ID
PDB 1cb1 "Master copy" parsed_1cb1
stop_
save_
save_global_Org_file_characteristics
_Constraint_stat_list.Sf_category constraint_statistics
_Constraint_stat_list.Entry_ID parsed_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 parsed_1cb1 1
1 1cb1.mr . . "MR format" 2 "dihedral angle" "Not applicable" "Not applicable" 0 parsed_1cb1 1
1 1cb1.mr . . n/a 3 comment "Not applicable" "Not applicable" 0 parsed_1cb1 1
1 1cb1.mr . . "MR format" 4 distance NOE simple 0 parsed_1cb1 1
1 1cb1.mr . . "MR format" 5 "nomenclature mapping" "Not applicable" "Not applicable" 0 parsed_1cb1 1
stop_
save_
save_MR_file_comment_1
_Org_constr_file_comment.Sf_category org_constr_file_comment
_Org_constr_file_comment.Entry_ID parsed_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 -------------------------------------------------------
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save_
save_MR_file_comment_3
_Org_constr_file_comment.Sf_category org_constr_file_comment
_Org_constr_file_comment.Entry_ID parsed_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_
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