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- PDB-28dn: CRYSTAL STRUCTURE ANALYSIS OF AN A(DNA) OCTAMER D(GTACGTAC) -

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Basic information

Entry
Database: PDB / ID: 28dn
TitleCRYSTAL STRUCTURE ANALYSIS OF AN A(DNA) OCTAMER D(GTACGTAC)
ComponentsDNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsCourseille, C. / Dautant, A. / Hospital, M. / Langlois D'Estaintot, B. / Precigoux, G. / Molko, D. / Teoule, R.
CitationJournal: Acta Crystallogr.,Sect.A / Year: 1990
Title: Crystal Structure Analysis of an A(DNA) Octamer d(GTACGTAC)
Authors: Courseille, C. / Dautant, A. / Hospital, M. / Langlois D'Estaintot, B. / Precigoux, G. / Molko, D. / Teoule, R.
History
DepositionMay 3, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 15, 1991Provider: 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*TP*AP*CP*GP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water1,00956
1
A: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')

A: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-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)42.500, 42.500, 24.790
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-44-

HOH

21A-50-

HOH

31A-52-

HOH

41A-60-

HOH

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Components

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


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


Mass: 18.015 Da / Num. of mol.: 56 / 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: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 293 K / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMoligonucleotide1drop
225 mMsodium cacodylate1drop
315 mM1dropMgCl2
48 mMspermine hydrochloride1drop
55 %(v/v)MPD1drop
630 %(v/v)MPD1reservoir
71

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Data collection

DiffractionMean temperature: 279 K
DetectorType: NICOLET / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. all: 2682 / Num. obs: 894 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Observed criterion σ(I): 1 / Num. measured all: 2682 / Rmerge(I) obs: 0.055

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementHighest resolution: 2.4 Å / σ(I): 1 /
RfactorNum. reflection
Rwork0.17 -
obs0.17 973
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 56 217
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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