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- PDB-178d: CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANIN... -

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Basic information

Entry
Database: PDB / ID: 178d
TitleCRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 8-HYDROXYDEOXYGUANINE.ADENINE BASE-PAIRS
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMcAuley-Hecht, K.E. / Leonard, G.A. / Gibson, N.J. / Thomson, J.B. / Watson, W.P. / Hunter, W.N. / Brown, T.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs.
Authors: McAuley-Hecht, K.E. / Leonard, G.A. / Gibson, N.J. / Thomson, J.B. / Watson, W.P. / Hunter, W.N. / Brown, T.
History
DepositionMay 19, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 4, 1994Provider: 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*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*(8OG)P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4072
Polymers7,4072
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.670, 40.490, 65.140
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*(8OG)P*GP*CP*G)-3')


Mass: 3703.417 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 %MPD1reservoir
21 mMoligonucleotide1drop
320 mMmagnesium chloride1drop
48 %(v/v)MPD1drop
51 mMspermine tetrahydrochloride1drop
612 mMsodium cacoylate1drop
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 9923 / Num. obs: 1965 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 5480 / % possible obs: 81 % / Redundancy: 2.8 % / Num. measured all: 9923 / Rmerge(I) obs: 0.068

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.168 1843
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 2 72 564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it2.4452.445
X-RAY DIFFRACTIONn_sugar_angle_it3.4153.415
X-RAY DIFFRACTIONn_phos_bond_it4.4964.496
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0060.006
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0140.014
X-RAY DIFFRACTIONn_phos_bond_d0.0050.005
X-RAY DIFFRACTIONn_phos_bond_angle_d0.010.01
X-RAY DIFFRACTIONn_plane_restr0.0050.005
X-RAY DIFFRACTIONn_chiral_restr0.2450.245
X-RAY DIFFRACTIONn_singtor_nbd0.070.07
X-RAY DIFFRACTIONn_multtor_nbd0.1750.175
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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