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- PDB-1d78: HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTA... -

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Basic information

Entry
Database: PDB / ID: 1d78
TitleHIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsThota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A.
Authors: Thota, N. / Li, X.H. / Bingman, C.A. / Sundaralingam, M.
#1: Journal: Biochemistry / Year: 1991
Title: Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure: Correlated Variations in Helical Parameters
Authors: Jain, S. / Zon, G. / Sundaralingam, M.
History
DepositionJun 12, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 22, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _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*GP*TP*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water66737
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A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')

A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*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 operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)32.182, 32.182, 78.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*TP*AP*CP*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.: 37 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 283.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
7MGCL212
Crystal grow
*PLUS
Temperature: 283 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %(v/v)MPD1drop
24 mM1dropMgCl2
32 mMspermine1drop
550 %MPD1reservoir
620 mM1reservoirMgCl2
4DNA1dropduplex
71

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Data collection

DiffractionMean temperature: 258 K
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→5 Å / Num. all: 7730 / Num. obs: 4365 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 5 Å / Num. all: 5261 / % possible obs: 86 % / Observed criterion σ(I): 2 / Num. measured all: 9036 / Rmerge(I) obs: 0.034

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.4→5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.198 4365
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 37 198
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 7730 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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