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3D Solution NMR Structure of the M9I Mutant of the HMG-Box Domain of the Human Male Sex Determining Factor SRY Complexed to DNA
SOLUTION NMR
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX500
500
2
Bruker
DRX600
600
3
Bruker
DRX750
750
NMR Refinement
Method
Details
Software
THE STRUCTURE WAS CALCULATED BY SIMULATED ANNEALING IN
TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. J. MAGN.
RESON., IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR
NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL
SHIFT RESTRAINTS (KUSZWESKI ET AL. J. MAGN. RESON. SERIES B
106, 92-96 (1995), J COUPLING RESTRAINTS (GARRETT ET AL. J.
MAGN. RESON. SERIES B 104, 99, 103 (1994); DIPOLAR COUPLING
RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998);
J.MAGN.RESON. 133, 216-221(1998)), AND RADIUS OF GYRATION
(KUSZEWSKI ET AL. JACS 121, 2337 (1999)). THE NON-BONDED
CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS
REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229,
129-136); THE DELPHIC TORSION ANGLE DATABASE POTENTIAL
(KUSZEWSKI & C J. MAGN. RESON. 146, 249 (2000)); AND THE
DELPHIC BASE-BASE POSITIONAL DATABASE POTENTIAL (KUSZEWSKI
ET AL. JACS 123, 3903 (2001)). IN THIS ENTRY THE SECOND TO
LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN
THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES (400 FOR THE
WILD TYPE COMPLEX) AND THE MEAN COORDINATE POSITIONS
(OBTAINED BY BEST FITTING TO RESIDUES 4-81 OF THE PROTEIN
AND 101-128 OF THE DNA).
THE ORIENTATION PROVIDED FOR THE MUTANT (1J47) RELATIVE
TO THE WILD TYPE (1J46) WAS OBTAINED BY BEST-FITTING TO
RESIDUES 4-81 OF THE PROTEIN.
WILD TYPE M9I MUTANT
PDB ID: 1J46 1J47
DEVIATIONS FROM IDEALIZED GEOMETRY:
BONDS 0.003 A 0.003 A
ANGLES 0.81 DEG 0.80 DEG
IMPROPERS 0.79 DEG 0.79 DEG
DEVIATIONS FROM EXPT RESTRAINTS
NOES (1795/1693) 0.04 A 0.03 A
TORSION ANGLES (433/429) 0.29 DEG 0.30 DEG
3JHNA COUPLINGS (70/66) 0.84 HZ 0.90 HZ
13C CHEMICAL SHIFTS (165/165) 0.99 PPM 0.95 PPM
HETERONUCLEAR DIPOLAR COUPLING R-FACTORS
(CLORE AND GARRETT J. AM. CHEM. SOC. 121, 9008-9012):
PROTEIN 1DNH (71/66) 5.5% 7.6%
PROTEIN 1DCH (67/67) 6.3% 10.0%
PROTEIN 1DNC' (68/62) 18.9% 28.9%
PROTEIN 2DHNC'(68/62) 18.8% 21.6%
DNA 1DNH (9/10) 10.2% 16.1%
DNA 1DCH (37/33) 11.2% 10.7%
DNA 1H-1H DIPOLAR
COUPLINGS (55/53) 0.56 HZ 0.75 HZ
% RESIDUES IN MOST FAVORABLE
REGION OF RAMACHADRAN MAP 94.7% 94.7%
X-PLOR NIH VERSION (HTTP://NMR.CIT.NIH.GOV)
NMR Ensemble Information
Conformer Selection Criteria
RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers Calculated Total Number
400
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1)
DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2)
DOUBLE RESONANCE AND HETERONUCLEAR FILTERED FOR DNA; (3)
QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (4) 2D,
3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED
NOE EXPERIMENTS; (4) 2D and 3D DOUBLE AND TRIPLE
RESONANCE EXPERIMENTS FOR DIPOLAR COUPLING MEASUREMENTS
IN LIQUID CRYSTALLINE MEDIUM OF 4.5-5% 3:1 DMPC:DHPC