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- PDB-2d95: LOW-TEMPERATURE STUDY OF THE A-DNA FRAGMENT D(GGGCGCCC) -

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Basic information

Entry
Database: PDB / ID: 2d95
TitleLOW-TEMPERATURE STUDY OF THE A-DNA FRAGMENT D(GGGCGCCC)
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: 2 Å
AuthorsEisenstein, M. / Hope, H. / Haran, T.E. / Frolow, F. / Shakked, Z. / Rabinovich, D.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.B / Year: 1988
Title: Low-temperature study of the A-DNA fragment d(GGGCGCCC)
Authors: Eisenstein, M. / Hope, H. / Haran, T.E. / Frolow, F. / Shakked, Z. / Rabinovich, D.
#1: 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.
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 1.3Feb 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
Water72140
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)42.740, 42.740, 24.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-35-

HOH

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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: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
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
3NA CACODYLATE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 115 K / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
130 %(v/v)MPD1
250 mMcacodylate1
315 mM1MgCl2
41
51
61

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. all: 2299 / Num. obs: 1694 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 2 /
RfactorNum. reflection
obs0.21 1694
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 40 201
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 1694 / σ(F): 2 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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