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SOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REGULARIZED MEAN COORDINATES
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
6.1
300
2
CBCANH
6.1
300
3
HNCO
6.1
300
4
C(CO)NH
6.1
300
5
H(CCO)NH
6.1
300
6
HCCH-COSY
6.1
300
7
HCCH-TOCSY
6.1
300
8
HNHA
6.1
300
9
15N-SEPARATED HOHAHA; QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; 3D 15N-SEPARATED NOE
6.1
300
10
3D 13C-SEPARATED NOE AND ROE
6.1
300
11
4D 15N/13C-SEPARATED NOE
6.1
300
12
4D 13C/13C-SEPARATED NOE EXPERIMENTS; 3D HCA(CO)N FOR THREE-BOND AMINIDE DEUTERIUM ISOTOPE SHIFTS; VARIOUS COUPLED 2D AND 3D SPECTRA TO MEASURE THE N-H
6.1
300
13
CA-H
6.1
300
14
C-H CA-C'
6.1
300
15
N-C'
6.1
300
16
HN-C' DIPOLAR COUPLINGS OBTAINED BY TAKING THE DIFFERENCE IN THE J SPLITTINGS IN ISOTROPIC MEDIUM
6.1
300
17
IN A LIQUID CRYSTALLINE MEDIUM (4% 3:1 DMPC:DHPC).
6.1
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DMX500
500
2
Bruker
DMX600
600
3
Bruker
DMX750
750
NMR Refinement
Method
Details
Software
simulated annealing
AVE.RMS DIFF. TO MEAN FOR ALL NON-H-ATOMS (RESIDUES
1:101)= 0.433636
AVE.RMS DIFF. TO MEAN FOR BACKBONE ATOMS (N, CA, C', O)
(RESIDUES 1:101)= 0.139826
RMS DEVIATIONS FOR BONDS, ANGLES, IMPROPERS, CDIH, NOE,
COUP 5.067337E-03, 0.712983, 0.667194, 0.157308,
1.428009E-02, 0.608909
C13CA AND CB SHIFTS RMS : 0.852581, 1.15742
JCOUP STATS: NON-GLY RESIDUES GLY
RMS-D: 0.608909 1.46813
BACKBONE DIPOLAR COUPLINGS NH CH CACO NCO HNCO
RMS : 0.466712 1.15058 1.29414 0.572019 1.2653
SIDECHAIN DIPOLAR COUPLINGS CH CH3S CH3D ARO
RMS DIPO_SIDE: 1.6875 0.796796 0.531907 0.160016
RMS FOR 1H SHIFTS: ALL ALPHA ALPHA_GLY METHYL(S)
METHYL(D) OTHER(S) OTHER(D)
RMS PROT: 0.263524 0.243015 0.23853 0.115892 0.148148
0.267304 0.300122
IN THE RESTRAINED REGULARIZED MEAN COORDINATES (2EZM) THE
LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN
THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN
COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA
STRUCTURES (2EZN) HAS NO MEANING. BEST FITTING TO GENERATE
THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 1-101.
NOTE THE OCCUPANCY FIELD HAS NO MEANING.
CNS
NMR Ensemble Information
Conformer Selection Criteria
REGULARIZED MEAN STRUCTURE
Conformers Calculated Total Number
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
THE 3D STRUCTURE OF CYANOVIRIN SOLVED BY
MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 2597
EXPERIMENTAL NMR RESTRAINTS: 419 SEQUENTIAL (|I- J|=1),
170 MEDIUM RANGE (1 < |I-J| <=5) AND 554 LONG RANGE
(|I-J| >5) INTERRESIDUES AND 19 INTRARESIDUE APPROXIMATE
INTERPROTON DISTANCE RESTRAINTS; 109 DISTANCE RESTRAINTS
FOR 55 H-BONDS; 339 TORSION ANGLE RESTRAINTS
(100 PHI, 98 PSI, 76 CHI1, 48 CHI2, 15 CHI3, 2 CHI4);
82 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 157
(82 CALPHA AND 75 CBETA) 13C SHIFT RESTRAINTS; 362 1H SHIFT
RESTRAINTS; AND 386 DIPOLAR COUPLING RESTRAINTS
(82 N-H, 76 C-H, 43 CA-C', 65 N-C' 62 HNC', 58 SIDE-CHAIN C-H).
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229,
129-136 USING THE PROGRAM CNS (BRUNGER ET AL. ACTA CRYST
SERIES D IN PRESS) 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), 1H CHEMICAL
SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B
107, 293-297; KUSZEWSKI ET AL. (1996) J. MAGN. RESON.
SERIES B 112, 79-81), AND DIPOLAR COUPLING (CLORE ET AL.
(1998) J. MAGN. RESON. 131, 159-162) RESTRAINTS, AND A
CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996)
PROTEIN SCI. 5, 1067-1080; KUSZEWSKI ET AL. (1997) J. MAGN.
RESON 125, 171-177).