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- PDB-295d: CRYSTAL AND SOLUTION STRUCTURES OF THE OLIGONUCLEOTIDE D(ATGCGCAT... -

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Entry
Database: PDB / ID: 295d
TitleCRYSTAL AND SOLUTION STRUCTURES OF THE OLIGONUCLEOTIDE D(ATGCGCAT)2: A COMBINED X-RAY AND NMR STUDY
ComponentsDNA (5'-D(*AP*TP*GP*CP*GP*CP*AP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsClark, G.R. / Brown, D.G. / Sanderson, M.R. / Chwalinski, T. / Neidle, S. / Veal, J.M. / Jones, R.L. / Wilson, W.D. / Zon, G. / Garman, E. / Stuart, D.I.
CitationJournal: Nucleic Acids Res. / Year: 1990
Title: Crystal and solution structures of the oligonucleotide d(ATGCGCAT)2: a combined X-ray and NMR study.
Authors: Clark, G.R. / Brown, D.G. / Sanderson, M.R. / Chwalinski, T. / Neidle, S. / Veal, J.M. / Jones, R.L. / Wilson, W.D. / Zon, G. / Garman, E. / Stuart, D.I.
History
DepositionMay 28, 1991Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 4, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
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(*AP*TP*GP*CP*GP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water93752
1
A: DNA (5'-D(*AP*TP*GP*CP*GP*CP*AP*T)-3')

A: DNA (5'-D(*AP*TP*GP*CP*GP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.406, 42.406, 24.902
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(*AP*TP*GP*CP*GP*CP*AP*T)-3')


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


Mass: 18.015 Da / Num. of mol.: 52 / 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: 46.68 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDCommon nameCrystal-ID
1MPD1
21

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Data collection

Diffraction sourceSource: ROTATING ANODE
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementRfactor obs: 0.177 / Highest resolution: 1.5 Å
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 52 213
Refinement
*PLUS
Highest resolution: 1.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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