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- PDB-243d: STRUCTURE OF THE DNA OCTANUCLEOTIDE D(ACGTACGT)2 -

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Basic information

Entry
Database: PDB / ID: 243d
TitleSTRUCTURE OF THE DNA OCTANUCLEOTIDE D(ACGTACGT)2
ComponentsDNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWilcock, D.J. / Adams, A. / Cardin, C.J. / Wakelin, L.P.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of the DNA octanucleotide d(ACGTACGT)2.
Authors: Wilcock, D.J. / Adams, A. / Cardin, C.J. / Wakelin, L.P.
History
DepositionJan 10, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 26, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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*CP*GP*TP*AP*CP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water36020
1
A: DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3')

A: DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*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)42.845, 42.845, 24.804
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*CP*GP*TP*AP*CP*GP*T)-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.: 20 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACODYLATE11
4MG ACETATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 291 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMDNA1drop
21.5 mMcacodylate1drop
31.25 mMmagnesium acetate1drop
42.5 mMsperine-4HCl1drop
56 %MPD1drop
630 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 0.7107
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.5→9 Å / Num. all: 24514 / Num. obs: 3962 / % possible obs: 88.7 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.0883
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 9 Å / % possible obs: 88.7 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
X-PLOR3refinement
XDSdata reduction
RefinementResolution: 1.9→5 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.177 --
obs0.177 1994 97.7 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 20 181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2

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