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- PDB-1d92: REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH G.T MI... -

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Basic information

Entry
Database: PDB / ID: 1d92
TitleREFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH G.T MISMATCHED BASE-PAIRS
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*TP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsHunter, W.N. / Kneale, G. / Brown, T. / Rabinovich, D. / Kennard, O.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Refined crystal structure of an octanucleotide duplex with G . T mismatched base-pairs.
Authors: Hunter, W.N. / Kneale, G. / Brown, T. / Rabinovich, D. / Kennard, O.
#1: Journal: Nature / Year: 1985
Title: High-Resolution Structure of a DNA Helix Containing Mismatched Base Pairs
Authors: Brown, T. / Kennard, O. / Kneale, G. / Rabinovich, D.
#2: Journal: J.Biomol.Struct.Dyn. / Year: 1985
Title: Structural Studies of DNA Fragments. The G.T Wobble Base Pair in A, B and Z DNA. The G.A Base Pair in B-DNA
Authors: Kennard, O.
History
DepositionOct 17, 1992Deposition 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8872
Polymers4,8872
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 45.200, 42.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2443.604 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4WATER12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
13 mMsodium cacodylate1
228 mM1MgCl2
31
41

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Data collection

DiffractionMean temperature: 275 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. obs: 2414
Reflection
*PLUS
Highest resolution: 2.25 Å / Rmerge(I) obs: 0.06

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.25→10 Å / σ(I): 2 /
RfactorNum. reflection
obs0.136 1924
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 0 52 376
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 10 Å / Num. reflection obs: 1924 / σ(I): 2 / Rfactor obs: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 85 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0260.015
X-RAY DIFFRACTIONn_angle_d0.0410.025
X-RAY DIFFRACTIONn_plane_restr0.020
X-RAY DIFFRACTIONn_mcbond_it2.5372.5
X-RAY DIFFRACTIONn_mcangle_it2.6760.3

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