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- PDB-1dnm: CRYSTAL STRUCTURE AND SEQUENCE-DEPENDENT CONFORMATION OF THE A.G ... -

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Basic information

Entry
Database: PDB / ID: 1dnm
TitleCRYSTAL STRUCTURE AND SEQUENCE-DEPENDENT CONFORMATION OF THE A.G MIS-PAIRED OLIGONUCLEOTIDE D(CGCAAGCTGGCG)
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*GP*CP*TP*GP*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
AuthorsWebster, G.D. / Sanderson, M.R. / Skelly, J.V. / Neidle, S. / Swann, P.F. / Li, B.F. / Tickle, I.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).
Authors: Webster, G.D. / Sanderson, M.R. / Skelly, J.V. / Neidle, S. / Swann, P.F. / Li, B.F. / Tickle, I.J.
History
DepositionJun 22, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 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*GP*CP*TP*GP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*GP*CP*TP*GP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3772
Polymers7,3772
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.290, 41.780, 64.760
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*GP*CP*TP*GP*GP*CP*G)-3')


Mass: 3688.405 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 46.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2 / Details: pH 7.20, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7.2 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.75 mMdodecamer1drop
225 mM1dropMgCl2
32.5 mMspermine1drop
430 mMsodium cacodylate1drop
532 %(v/w)MPD1reservoir
61

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SEALED TUBE
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 9842 / Num. obs: 2495 / Rmerge(I) obs: 0.119
Reflection
*PLUS
Num. obs: 1710 / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.119 / Num. measured all: 2495

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å / σ(F): 3 /
RfactorNum. reflection
obs0.193 1710
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 0 47 537
Refinement
*PLUS
σ(F): 3 / Highest resolution: 2.5 Å / Num. reflection obs: 1710 / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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