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- PDB-2d94: THE CONFORMATION OF THE DNA DOUBLE HELIX IN THE CRYSTAL IS DEPEND... -

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Basic information

Entry
Database: PDB / ID: 2d94
TitleTHE CONFORMATION OF THE DNA DOUBLE HELIX IN THE CRYSTAL IS DEPENDENT ON ITS ENVIRONMENT
ComponentsDNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsShakked, Z. / Guerstein-Guzikevich, G. / Eisenstein, M. / Frolow, F. / Rabinovich, D.
Citation
Journal: Nature / Year: 1989
Title: The conformation of the DNA double helix in the crystal is dependent on its environment.
Authors: Shakked, Z. / Guerstein-Guzikevich, G. / Eisenstein, M. / Frolow, F. / Rabinovich, D.
#1: Journal: 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
DepositionJul 13, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 14, 2024Group: 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*CP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water1,58588
1
A: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)43.280, 43.280, 24.660
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*GP*CP*GP*CP*CP*C)-3')


Mass: 2428.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 292.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Method: unknown / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaDetails
12.8 mMDNA1
27 mM1MgCl2
30.1 mMspermine-4HCl1
420 %MPD1
550 mMsodium cacodylate1
640 %MPD1pH6.5
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: NONIUS CAD4 / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 2027 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.162 2027
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 88 249
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 2027 / σ(F): 2 / Rfactor obs: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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