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- PDB-1d98: THE STRUCTURE OF AN OLIGO(DA).OLIGO(DT) TRACT AND ITS BIOLOGICAL ... -

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Basic information

Entry
Database: PDB / ID: 1d98
TitleTHE STRUCTURE OF AN OLIGO(DA).OLIGO(DT) TRACT AND ITS BIOLOGICAL IMPLICATIONS
Components
  • DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNelson, H.C.M. / Finch, J.T. / Luisi, B.F. / Klug, A.
CitationJournal: Nature / Year: 1987
Title: The structure of an oligo(dA).oligo(dT) tract and its biological implications.
Authors: Nelson, H.C. / Finch, J.T. / Luisi, B.F. / Klug, A.
History
DepositionOct 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 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(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.400, 40.700, 65.800
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*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')


Mass: 3689.446 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')


Mass: 3635.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 mMDNA1drop
210.0 mMmagnesium acetate1drop
30.5 mMspermine-HCl1drop
450 %(v/v)MPD1drop
537.5 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 277 K
DetectorType: HILGER-WATTS / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 2572
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 3 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(I): 0.5 /
RfactorNum. reflection
obs0.2 2003
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 27 513
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 2003 / σ(I): 0.5
Solvent computation
*PLUS
Displacement parameters
*PLUS

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