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- PDB-1d99: STRUCTURAL FEATURES AND HYDRATION OF A DODECAMER DUPLEX CONTAININ... -

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Basic information

Entry
Database: PDB / ID: 1d99
TitleSTRUCTURAL FEATURES AND HYDRATION OF A DODECAMER DUPLEX CONTAINING TWO C.A MISPAIRS
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*CP*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
AuthorsHunter, W.N. / Brown, T. / Kennard, O.
Citation
Journal: Nucleic Acids Res. / Year: 1987
Title: Structural features and hydration of a dodecamer duplex containing two C.A mispairs.
Authors: Hunter, W.N. / Brown, T. / Kennard, O.
#1: Journal: Nature / Year: 1986
Title: Structure of an Adenine. Cytosine Base Pair in DNA and Its Implications for Mismatch Repair
Authors: Hunter, W.N. / Brown, T. / Anand, N.N. / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,2952
Polymers7,2952
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.370, 41.440, 65.200
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*TP*TP*CP*GP*CP*G)-3')


Mass: 3647.393 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MG ACETATE11
5SPERMINE11
6WATER12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Details: referred to 'Wing, R..', (1980) 'Nature', 287, 755-758
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1DNA1drop
2magnesium acetate1drop
3spermine hydrochloride molecule1drop
420-30 %MPD1reservoir
51
61

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Data collection

DiffractionMean temperature: 277 K
DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 2452 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2.5 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(I): 2 /
RfactorNum. reflection
obs0.19 2029
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 0 78 562
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(I): 2 / Num. reflection obs: 2029 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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