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- PDB-1d91: G.T BASE PAIRS IN A DNA HELIX. THE CRYSTAL STRUCTURE OF D(G-G-G-G... -

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Basic information

Entry
Database: PDB / ID: 1d91
TitleG.T BASE PAIRS IN A DNA HELIX. THE CRYSTAL STRUCTURE OF D(G-G-G-G-T-C-C-C)
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKneale, G. / Brown, T. / Kennard, O. / Rabinovich, D.
CitationJournal: J.Mol.Biol. / Year: 1985
Title: G . T base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C).
Authors: Kneale, G. / Brown, T. / Kennard, O. / Rabinovich, D.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8872
Polymers4,8872
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.710, 44.710, 42.400
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*TP*CP*CP*C)-3')


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
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
2MGCL211
3NA CACODYLATE11
4WATER12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
10.4 mMDNA1
260 mM1MgCl2
320 mMsodium cacodylate1
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: 2.1 Å / Num. obs: 2898
Reflection
*PLUS
Highest resolution: 2.1 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.145 2486
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 0 104 428
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection obs: 2486 / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS

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