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Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Experiment
1MK6
SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE
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NMR Restraints (Text)
NMR Restraints (gz)
V2 NMR Restraints (gz)
SOLUTION NMR Experimental Data
Experimental Details
Sample Conditions
Sample Contents
80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer
Solvent
For observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C.
Ionic Strength
0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O
pH
7.4
Pressure
ATM
Temperature (K)
278
Experiment(s):
2D NOESY, 2D TOCSY, DQF-COSY, P-COSY, T1
Spectrometer Information
Manufacturer
Model
Field Strength
Bruker
DRX
500.0
Bruker
DRX
600.0
Bruker
DRX
800.0
NMR Refinement
Method
distance geometry : MardiGras; simulated annealing molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing and Molecular Dynamics matrix relaxation : CORMA;
Details
There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA restraints
NMR Ensemble Information
Conformer Selection Criteria
Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.
Conformers Calculated Total Number
20
Conformers Submitted Total Number
1
Representative Model Choice Rationale
1
n/a
Additional NMR Experimental Information
1
40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported
Computation: NMR Software
#
Classification
Software Name
Author
1
processing version: 97, 2000
FELIX
Accelyris, Inc., San Diego, CA
2
collection version: 4.0
XWINNMR
Bruker
3
data analysis version: 3.2
MARDIGRAS
Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487
4
refinement version: 3.1
X-PLOR
A.T.Brunger
5
structure solution version: 6.0
AMBER
Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280
6
data analysis version: 4.0
CORMA
Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426.
7
structure solution version: 2000
INSIGHTII
Accelyris, Inc., San Diego, CA
8
processing version: 1998
GAUSSIAN 98
Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.