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- PDB-1vt7: Structures of the mismatched duplex D(GGGTGCCC) -

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Basic information

Entry
Database: PDB / ID: 1vt7
TitleStructures of the mismatched duplex D(GGGTGCCC)
ComponentsDNA (5'-D(*GP*GP*GP*TP*GP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRabinovich, D. / Haran, T. / Eisenstein, M. / Shakked, Z.
CitationJournal: J.Mol.Biol. / Year: 1988
Title: Structures of the mismatched duplex d(GGGTGCCC) and one of its Watson-Crick analogues d(GGGCGCCC).
Authors: Rabinovich, D. / Haran, T. / Eisenstein, M. / Shakked, Z.
History
DepositionDec 2, 1996Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Dec 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*GP*TP*GP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*TP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8872
Polymers4,8872
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.620, 45.620, 40.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2443.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligomer
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: MPD, MgCl2, spermine, sodium cacodylate, pH 7.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38MGCL21917
411SPERMINE_HCL112110
514NA CACODYLATE115113
617WATER118216
720MPD121219

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceWavelength: 1.5418
DetectorType: NONIUS CAD4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 2000

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.152 -
obs0.152 1362
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 0 43 367

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