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- PDB-1vt9: The structure and hydration of the A-DNA fragment D(GGGTACCC) at ... -

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Basic information

Entry
Database: PDB / ID: 1vt9
TitleThe structure and hydration of the A-DNA fragment D(GGGTACCC) at room temperature and low temperature
ComponentsDNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsEisenstein, M. / Frolow, F. / Shakked, Z. / Rabinovich, D.
CitationJournal: Nucleic Acids Res. / Year: 1990
Title: The structure and hydration of the A-DNA fragment d(GGGTACCC) at room temperature and low temperature.
Authors: Eisenstein, M. / Frolow, F. / Shakked, Z. / Rabinovich, D.
History
DepositionApr 11, 1991Deposition 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*AP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*TP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area3090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 46.800, 44.520
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*AP*CP*CP*C)-3')


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 277 K
Details: MPD, MgCl2, spermine, sodium cacodylate, temperature 277K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38MGCL21917
411SPERMINE_HCL112110
514NA CACODYLATE115113

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SEALED TUBE
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 1818 / Num. obs: 1582 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.119 -
obs0.119 1545
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 89 411

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