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- PDB-1vtb: THE HEXAGONAL CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTGTACAC) ... -

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Basic information

Entry
Database: PDB / ID: 1vtb
TitleTHE HEXAGONAL CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTGTACAC) AND ITS COMPARISON WITH THE TETRAGONAL STRUCTURE CORRELATED VARIATIONS IN HELICAL PARAMETERS
ComponentsDNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsJain, S.C. / Zon, G. / Sundaralingam, M.
Citation
Journal: Biochemistry / Year: 1991
Title: The Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure Correlated Variations in Helical Parameters
Authors: Jain, S.C. / Zon, G. / Sundaralingam, M.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Effect of Crystal Packing Environment on Conformation of the DNA Duplex
Authors: Jain, S. / Sundaralingam, M.
#2: Journal: Biochemistry / Year: 1989
Title: Base Only Binding of Spermine in the Deep Groove of the A-DNA Octamer d(GTGTACAC)
Authors: Jain, S. / Zon, G. / Sundaralingam, M.
History
DepositionMay 28, 1991Deposition 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water90150
1
A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area740 Å2
ΔGint-5 kcal/mol
Surface area3070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.400, 32.400, 79.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 278.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38MGCL21917
411SPERMINE112110
514WATER115213
617MPD118216

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Data collection

Diffraction sourceSource: ROTATING ANODE
DetectorType: ARNDT-WONACOTT / Detector: OSCILLATION CAMERA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 8156 / Num. obs: 1683 / Observed criterion σ(I): 1.5

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.127 1561
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 50 211

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