| simulated annealing |
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER)
MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL.
(1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON
CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON.
SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL
DATABASE
POTENTIAL (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 SECOND DNA BINDING
DOMAIN OF HMG-I(Y)
COMPLEXED TO DNA WAS SOLVED BY
MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR
(A) PROTEIN: 71 SEQUENTIAL (|I-J|=1), 4 MEDIUM
RANGE (1 < |I-J| >=5) AND 64 INTRARESIDUE
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL
36 TORSION ANGLE RESTRAINTS
13 THREE-BOND HN-HA AND 8 THREE_BOND COCO COUPLING
CONSTANT RESTRAINTS; 39 (21 CALPHA AND 18 CBETA) 13C
SHIFT RESTRAINTS.
(B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND
33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42
DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 136
TORSION ANGLE RESTRAINTS
(C) 73 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(D) 5 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
(E) 20 'REPULSIVE' RESTRAINTS
THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED
MEAN STRUCTURE. THE LAST NUMERIC COLUMN REPRESENTS THE
RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES
FOUND IN PDB ENTRY 2EZE ABOUT THE MEAN COORDINATE
POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA
STRUCTURES HAS NO MEANING.
RESIDUES 3 - 27 OF THE PROTEIN CORRESPOND TO RESIDUES 51 -
75 OF INTACT HMG-I(Y). RESIDUES 3 - 5 AND 20 - 27 ARE
DISORDERED. ONLY RESIDUES 3 - 23 ARE PROVIDED FOR THE
RESTRAINED REGULARIZED MEAN STRUCTURE. |
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