| simulated annealing |
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING
THE PROGRAM X-PLOR MODIFIED TO INCORPORATE COUPLING
CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON.
SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS
(KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92
- 96) RESTRAINTS, DIPOLAR COUPLING RESTRAINTS (TJANDRA ET
AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A
CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC
ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080
AND (1997) J. MAGN. RESON. 125, 171-177)
THE 3D STRUCTURE OF THE COMPLEX OF THE WILD TYPE AREA
DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL
HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE
FOLLOWING 1098 EXPERIMENTAL RESTRAINTS
(A) PROTEIN: 119 SEQUENTIAL (|I-J|=1), 49 SHORT RANGE (1
< |I-J| >=5), 68 LONG RANGE (|I-J|>5), AND 64 INTRARESIDUE
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 124
TORSION ANGLE RESTRAINTS (61 PHI, 8 PSI, 39 CHI1, 15 CHI2,
AND 1 CHI3), 41 THREE-BOND HN-HA COUPLING CONSTANT
RESTRAINTS; NULL 77 (41 CALPHA AND 36 CBETA) 13C CHEMICAL
SHIFT RESTRAINTS; NULL 48 RESIDUAL N-H DIPOLAR COUPLING
RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE
HYDROGEN BONDS.
(B) DNA: 75 INTRARESIDUE, 115 SEQUENTIAL INTRASTRAND AND
20 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 66
DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170
TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING
VALUES CHARACTERISTIC OF BOTH A AND B DNA.
(C) 48 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
(E) 8 'REPULSIVE' RESTRAINTS
(F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS
BETWEEN ARG 24 AND BASE OF GUA5.
THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED
MEAN STRUCTURE AND THE LAST NUMERIC COLUMN REPRESENTS THE
RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
FOUND IN PDB ENTRY 5GAT ABOUT THE MEAN COORDINATE
POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA
STRUCTURES HAS NO MEANING.
THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL
AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR:
POINT 1 115.014-147.742 -73.887
POINT 2 115.768-146.457 -73.538 |
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