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- PDB-8bna: BINDING OF HOECHST 33258 TO THE MINOR GROOVE OF B-DNA -

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Basic information

Entry
Database: PDB / ID: 8bna
TitleBINDING OF HOECHST 33258 TO THE MINOR GROOVE OF B-DNA
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyChem-HT / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPjura, P.E. / Grzeskowiak, K. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Binding of Hoechst 33258 to the minor groove of B-DNA.
Authors: Pjura, P.E. / Grzeskowiak, K. / Dickerson, R.E.
#1: Journal: J.Med.Chem. / Year: 1986
Title: Isohelical Analysis of DNA Groove-Binding Drugs
Authors: Goodsell, D. / Dickerson, R.E.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G
Authors: Kopka, M.L. / Yoon, C. / Goodsell, D.S. / Pjura, P. / Dickerson, R.E.
#3: Journal: To be Published
Title: Drugs and Minor Groove Binding in B-DNA Netropsin and Hoechst 33258
Authors: Kopka, M.L. / Pjura, P.E. / Goodsell, D.S. / Dickerson, R.E.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin
Authors: Kopka, M.L. / Yoon, C. / Goodsell, D.S. / Pjura, P. / Dickerson, R.E.
#5: Journal: Nature / Year: 1980
Title: Crystal Structure Analysis of a Complete Turn of B-DNA
Authors: Wing, R. / Drew, H.R. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionAug 29, 1986Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 15, 1987Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 2, 2014Group: Other
Revision 1.4Feb 14, 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*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7764
Polymers7,3272
Non-polymers4492
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.040, 40.330, 65.850
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*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-HT / 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33258


Mass: 424.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N6O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE ACETATE11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.21 mMDNA1drop
20.21 mMHoechst 332581drop
35.38 mM1dropMg(OAc)2
40.21 mMspermine acetate1drop
520 %(w/v)MPD1drop
635 %1reservoir

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Data collection

DetectorType: SYNTEX P1 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 3487 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.2 Å / Observed criterion σ(I): 0.28

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.191 3594
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL DRUG ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 33 174 693
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor all: 0.191 / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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