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- PDB-1vt6: Molecular structure of the octamer D(G-G-C-C-G-G-C-C) modified A-DNA -

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Basic information

Entry
Database: PDB / ID: 1vt6
TitleMolecular structure of the octamer D(G-G-C-C-G-G-C-C) modified A-DNA
ComponentsDNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsWang, A.H.-J. / Fujii, S. / Van Boom, J.H. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA.
Authors: Wang, A.H. / Fujii, S. / van Boom, J.H. / Rich, A.
History
DepositionAug 18, 1988Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')

A: DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area3100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.060, 42.060, 25.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')


Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized oligomer

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growpH: 7 / Details: Sodium cacodylate, spermine, MgCl2, pH 7.00
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25NA CACODYLATE1614
38SPERMINE1917
411MGCL2112110
514WATER115213

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Data collection

DiffractionMean temperature: 265 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 1224

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Processing

RefinementHighest resolution: 2.25 Å / σ(I): 3 /
RfactorNum. reflection
Rwork0.174 -
obs0.174 920
Refinement stepCycle: LAST / Highest resolution: 2.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 0 161

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