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- PDB-1dnh: THE MOLECULAR STRUCTURE OF THE COMPLEX OF HOECHST 33258 AND THE D... -

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Basic information

Entry
Database: PDB / ID: 1dnh
TitleTHE MOLECULAR STRUCTURE OF THE COMPLEX OF HOECHST 33258 AND THE DNA DODECAMER D(CGCGAATTCGCG)
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: 2.25 Å
AuthorsTeng, M.-K. / Usman, N. / Frederick, C.A. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 1988
Title: The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG).
Authors: Teng, M.K. / Usman, N. / Frederick, C.A. / Wang, A.H.
History
DepositionFeb 16, 1988Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model / Derived calculations
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_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)7,7513
Polymers7,3272
Non-polymers4241
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.230, 40.580, 66.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: NO DISORDERED DRUG

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.UnitCommon nameSol-IDDetailsChemical formula
11.2 mMDNA dodecamerdropsingle strand
220 mMsodium cacodylatedrop
41 mMspermine tetrachloridedrop
51.2 mMHoechst 33258drop
612 %drop
750 %MPDreservoir
3mMdropMgCl2

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 3634 / Observed criterion σ(I): 0

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.25→20 Å / σ(F): 2 /
RfactorNum. reflection
obs0.157 2000
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 32 126 644
Refinement
*PLUS
σ(F): 2 / Highest resolution: 2.25 Å / Lowest resolution: 20 Å / Num. reflection obs: 2000 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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