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- PDB-1d24: CRYSTAL AND MOLECULAR STRUCTURE OF A DNA DUPLEX CONTAINING THE CA... -

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Basic information

Entry
Database: PDB / ID: 1d24
TitleCRYSTAL AND MOLECULAR STRUCTURE OF A DNA DUPLEX CONTAINING THE CARCINOGENIC LESION O6-METHYLGUANINE
ComponentsDNA (5'-D(*CP*GP*CP*(6OG)P*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGinell, S.L. / Kuzmich, S. / Jones, R.A. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1990
Title: Crystal and molecular structure of a DNA duplex containing the carcinogenic lesion O6-methylguanine.
Authors: Ginell, S.L. / Kuzmich, S. / Jones, R.A. / Berman, H.M.
History
DepositionAug 29, 1990Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 7, 1992Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6482
Polymers3,6482
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.850, 30.870, 43.980
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*(6OG)P*CP*G)-3')


Mass: 1824.232 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.66 Å3/Da / Density % sol: 25.93 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
130 mMsodium cacodylate1drop
30.5 mMspermine tetrahydrochloride1drop
410-20 %MPD1drop
52 mMDNA1drop
630 %MPD1reservoir
71
2mM1dropMgCl2

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 1597 / Num. obs: 1246 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0693
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 5557 / Num. obs: 1597 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0693 / Num. measured all: 1246

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.9→8 Å /
RfactorNum. reflection
obs0.19 1217
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 2 60 302
Refine LS restraints
Refine-IDTypeDev ideal
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_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
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_d0.014
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.027
X-RAY DIFFRACTIONn_phos_bond_d0.051
X-RAY DIFFRACTIONn_phos_bond_angle_d0.048
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Rfactor obs: 0.19 / Num. reflection obs: 1217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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