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- PDB-114d: INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 114d
TitleINOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX
ComponentsDNA (5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*AP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsCorfield, P.W.R. / Hunter, W.N. / Brown, T. / Robinson, P. / Kennard, O.
CitationJournal: Nucleic Acids Res. / Year: 1987
Title: Inosine.adenine base pairs in a B-DNA duplex.
Authors: Corfield, P.W. / Hunter, W.N. / Brown, T. / Robinson, P. / 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*IP*AP*AP*TP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3452
Polymers7,3452
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.850, 41.990, 65.100
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*IP*AP*AP*TP*TP*AP*GP*CP*G)-3')


Mass: 3672.403 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
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
4MGCL211
5SPERMINE11
Crystal grow
*PLUS
pH: 7.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
10.5 mMDNA duplex1
27.5 mMsodium cacodylate1
320 mM1MgCl2
41.0 mMspermine1
515 %(v/v)MPD1

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Data collection

DiffractionMean temperature: 277 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 2207 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.19 2105
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 0 64 552
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(I): 1 / Rfactor obs: 0.19
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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