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- PDB-153d: CRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, D(CGAGAATTC(O6ME)GCG)... -

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Basic information

Entry
Database: PDB / ID: 153d
TitleCRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, D(CGAGAATTC(O6ME)GCG)2, CONTAINING A CARCINOGENIC O6-METHYLGUANINE
ComponentsDNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsGinell, S.L. / Vojtechovsky, J. / Gaffney, B. / Jones, R. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine
Authors: Ginell, S.L. / Vojtechovsky, J. / Gaffney, B. / Jones, R. / Berman, H.M.
History
DepositionDec 16, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: 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 / 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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')
B: DNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4032
Polymers7,4032
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.130, 40.450, 64.510
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*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')


Mass: 3701.444 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 2924

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.9→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.169 1031
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 2 49 541
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_it0.532
X-RAY DIFFRACTIONn_sugar_angle_it0.792
X-RAY DIFFRACTIONn_phos_bond_it3.634
X-RAY DIFFRACTIONn_phos_angle_it2.638
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0120.02
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0220.025
X-RAY DIFFRACTIONn_phos_bond_d0.0230.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0240.025
X-RAY DIFFRACTIONn_plane_restr0.0120.02
X-RAY DIFFRACTIONn_chiral_restr0.090.1
X-RAY DIFFRACTIONn_singtor_nbd0.130.3
X-RAY DIFFRACTIONn_multtor_nbd0.180.3
X-RAY DIFFRACTIONn_xhyhbond_nbd

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