NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | program | type |
|
|
2630 |
1cb1   |
390 | cing | 1-original | MR format | 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 -------------------------------------------------------
Contact the webmaster for help, if required. Sunday, April 28, 2024 10:39:13 AM GMT (wattos1)