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N-TERMINAL CONSTANT REGION OF THE NUCLEAR ENVELOPE PROTEIN LAP2
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
RESTRAINED SIMULATED IN TORSION ANGLE SPACE
THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. J. MAGN. RESON. SERIES B 106, 92-96 (1995)), THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUs OF GYRATION (KUSZEWSKI ET AL. (1999), AND A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136).
IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE
RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED
ANNEALING STRUCTURES AND THE MEAN COORDINATE
POSITIONS. ONLY COORDINATES FOR RESIDUES 1-50 (LAP2-N)
and 111-153 (LAP2-C) ARE PROVIDED. THE LINKER CONNECTING
THESE TWO DOMAINS IS COMPLETELY DISORDERED.
LIKEWISE THE C-TERMINAL RESIDUES (154-168) ARE DISORDERED.
SINCE THE TWO DOMAINS, LAP2-N AND LAP2-C, REORIENT
ESSENTIALLY INDEPENDENTLY IN SOLUTION, THE COORDINATES
OF THE TWO DOMAINS HAVE BEEN BEST-FITTED TO EACH OTHER
SINCE THEY ARE STRUCTURALY VERY SIMILAR. THE LAP2-N
DOMAIN BINDS DNA. THE LAP2-C DOMAIN BINDS THE
BARRIER-TO-AUTOINTEGRATION FACTOR BAF.
Structural Statistics:
---------------------------------------------------------
LAP2-N LAP2-C
---------------------------------------------------------
DEVIATIONS FROM IDEALIZED GEOMETRY:
BONDS 0.003 A 0.003 A
ANGLES 0.48 DEG 0.54 DEG
IMPROPERS 0.49 DEG 0.39 DEG
DEVIATIONS FROM EXPT RESTRAINTS (LAP2-N/LAP2-C)
NOES (395/401) 0.024 A 0.012 A
TORSION ANGLES (151/121) 0.49 DEG 0.13 DEG
13C CHEMICAL SHIFTS (105/91) 0.92 PPM 0.81 PPM
DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999)
J. AM. CHEM. SOC. 121, 9008-9012):
1DNH (39/34) 6.4% 2.9%
1DCH (36/29) 6.4% 1.9%
1DNC' (24/19) 28.2% 26.2%
2DHNC' (24/20) 30.1% 25.3%
% RESIDUES IN MOST FAVORABLE
REGION OF RAMACHADRAN MAP 84.1% 89.0%
NOTE: THE ALIGNMENT TENSOR FOR LAP2-N and LAP2-C ARE
DIFFERENT DUE TO THE FACT THAT THE TWO DOMAINS ARE
ORIENTED INDEPENDENTLY BY THE PHAGE LIQUID
CRYSTALLINE MEDIUM.
X-PLOR NIH VERSION (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN PUB/CLORE/XPLOR_NIH or AT HTTP://NMR.CIT.NIH.GOV)
NMR Ensemble Information
Conformer Selection Criteria
RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers Calculated Total Number
20
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) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (3) 3D SEPARATED NOE EXPERIMENTS; (4) 2D and 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF PHAGE PF1.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
refinement
X-PLOR NIH VERSION (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN PUB/CLORE/XPLOR_NIH or AT HTTP://NMR.CIT.NIH.GOV)
CLORE, KUSZEWSKI AND SCHWIETERS. adapted from Brunger (general XPLOR)