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- PDB-1d32: DRUG-INDUCED DNA REPAIR: X-RAY STRUCTURE OF A DNA-DITERCALINIUM C... -

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Basic information

Entry
Database: PDB / ID: 1d32
TitleDRUG-INDUCED DNA REPAIR: X-RAY STRUCTURE OF A DNA-DITERCALINIUM COMPLEX
ComponentsDNA (5'-D(*CP*GP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyDITERCALINIUM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsGao, Q. / Williams, L.D. / Egli, M. / Rabinovich, D. / Chen, S.-L. / Quigley, G.J. / Rich, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex.
Authors: Gao, Q. / Williams, L.D. / Egli, M. / Rabinovich, D. / Chen, S.L. / Quigley, G.J. / Rich, A.
#1: Journal: Biochemistry / Year: 1992
Title: DNA-Ditercalinium Interactions: Implications for Recognition of Damaged DNA
Authors: Williams, L.D. / Gao, Q.
History
DepositionJan 23, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1033
Polymers2,3842
Non-polymers7191
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.880, 26.880, 82.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DIT / DITERCALINIUM


Mass: 718.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H50N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4NH4 ACETATE11
5SPERMINE11
6MGCL211
7WATER12
8MPD12
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.7 mMDNA1drop
216.8 mMsodium cacodylate1drop
314 mMammonium acetate1drop
40.3 mMspermine tetrachloride1drop
50.8 mMmagnesium chloride1drop
66 %MPD1drop
70.2 mMditercalinium1drop
830 %1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 2211 / Observed criterion σ(F): 3
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 2 Å / Observed criterion σ(F): 3

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→2 Å / σ(F): 3 /
RfactorNum. reflection
obs0.225 542
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL DRUG ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 158 54 83 295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.019
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_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
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: 1.7 Å / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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