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- PDB-311d: THE ROLE OF HYDROGEN BONDING IN MINOR-GROOVE DRUG-DNA RECOGNITION... -

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Basic information

Entry
Database: PDB / ID: 311d
TitleTHE ROLE OF HYDROGEN BONDING IN MINOR-GROOVE DRUG-DNA RECOGNITION. STRUCTURE OF A BIS-AMIDINIUM DERIVATIVE OF HOECHST 33258 COMPLEXED TO THE DODECANUCLEOTIDE D(CGCGAATTCGCG)2
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-HT2 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsClark, G.R. / Boykin, D.W. / Czarny, A. / Neidle, S.
CitationJournal: Nucleic Acids Res. / Year: 1997
Title: Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.
Authors: Clark, G.R. / Boykin, D.W. / Czarny, A. / Neidle, S.
History
DepositionFeb 4, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 11, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

Downloads & links

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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)7,7213
Polymers7,3272
Non-polymers3941
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.750, 40.560, 66.260
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-HT2 / 5-AMIDINO-2-[2-(4-AMIDINOPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE / BIS-AMIDINIUM DERIVATIVE OF HOECHST 33258


Mass: 394.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal grow
*PLUS
Temperature: 286 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %MPD1drop
21 mMDIBIZ1drop
33 mM1dropMgCl2
40.5 mMspermine1drop
51 mMdodecamer1drop
640 %MPD1reservoir

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Data collection

DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Oct 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 2954 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. all: 3740 / Num. obs: 3315 / % possible obs: 89 % / Observed criterion σ(F): 2

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 2954
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 30 77 593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.46
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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