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- PDB-183d: X-RAY STRUCTURE OF A DNA DECAMER CONTAINING 7, 8-DIHYDRO-8-OXOGUANINE -

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Basic information

Entry
Database: PDB / ID: 183d
TitleX-RAY STRUCTURE OF A DNA DECAMER CONTAINING 7, 8-DIHYDRO-8-OXOGUANINE
ComponentsDNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsLipscomb, L.A. / Peek, M.E. / Morningstar, M.L. / Verghis, S.M. / Miller, E.M. / Rich, A. / Essigmann, J.M. / Williams, L.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.
Authors: Lipscomb, L.A. / Peek, M.E. / Morningstar, M.L. / Verghis, S.M. / Miller, E.M. / Rich, A. / Essigmann, J.M. / Williams, L.D.
History
DepositionAug 1, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 27, 1995Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,0621
Polymers3,0621
Non-polymers00
Water75742
1
A: DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')

A: DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1242
Polymers6,1242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)32.270, 25.560, 34.710
Angle α, β, γ (deg.)90.00, 115.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*CP*CP*AP*(8OG)P*CP*GP*CP*TP*GP*G)-3')


Mass: 3061.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: pH 7.60, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3BIS-TRIS-PROPANE_HCL11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.9 mMDNA1dropsingle stranded
220 mMTris-HCl1drop
35 %methylpentanediol1drop
4133 mM1dropMgCl2
530 %methylpentanediol1reservoir
61

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. all: 12930 / Num. obs: 3290 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.6 Å / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0552

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.6→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.234 --
obs0.234 3290 95.4 %
Refine Biso
ClassRefine-ID
ALL ATOMSX-RAY DIFFRACTION
ALL WATERSX-RAY DIFFRACTION
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 203 1 42 246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.6

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