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- PDB-112d: MOLECULAR STRUCTURE OF THE G.A BASE PAIR IN DNA AND ITS IMPLICATI... -

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Basic information

Entry
Database: PDB / ID: 112d
TitleMOLECULAR STRUCTURE OF THE G.A BASE PAIR IN DNA AND ITS IMPLICATIONS FOR THE MECHANISM OF TRANSVERSION MUTATIONS
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrown, T. / Hunter, W.N. / Kneale, G. / Kennard, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations.
Authors: Brown, T. / Hunter, W.N. / Kneale, G. / Kennard, O.
History
DepositionJan 4, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3752
Polymers7,3752
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.690, 41.960, 65.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3687.417 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MG ACETATE11
5SPERMINE11
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
10.5 mMDNA duplex1
27.4 mMsodium cacodylate1
324 mM1Mg(OAc)2
41.0 mMspermine1
518 %(v/v)MPD1

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Data collection

DiffractionMean temperature: 278 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 2707 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.5 Å / Observed criterion σ(I): 0

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(I): 2 /
RfactorNum. reflection
obs0.17 1298
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 0 83 573
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(I): 2 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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