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- PDB-263d: ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL... -

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Basic information

Entry
Database: PDB / ID: 263d
TitleISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyChem-TBZ / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsClark, G.R. / Gray, E.J. / Neidle, S. / Li, Y.-H. / Leupin, W.
Citation
Journal: Biochemistry / Year: 1996
Title: Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.
Authors: Clark, G.R. / Gray, E.J. / Neidle, S. / Li, Y.H. / Leupin, W.
#1: Journal: Nucleic Acids Res. / Year: 1994
Title: Sequence-Dependent Effects in Drug-DNA Interaction: The Crystal Structure of Hoechst 33258 Bound to the d(CGCAAATTTGCG)2 Duplex
Authors: Spink, N. / Skelly, J.V. / Neidle, S.
#2: Journal: Eur.J.Biochem. / Year: 1994
Title: Three-Dimensional Crystal Structure of the A-Tract DNA Dodecamer d(CGCAAATTTGCG) Complexed with the Minor-Groove-Binding Drug Hoechst 33258
Authors: Vega, M.C. / Saez, I.G. / Aymami, J. / Eritja, R. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Coll, M.
History
DepositionSep 27, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 15, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8663
Polymers7,3252
Non-polymers5421
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.700, 40.820, 64.900
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*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-TBZ / 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE / TRIBIZ / TRIS(BENZIMIDAZOLE) DERIVATIVE


Mass: 541.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29N8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 286.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.5 %MPD1drop
20.9 mMTRIBIZ1drop
354.5 mM1dropMgCl2
40.2 mMspermine1drop
50.36 mMdodecamer1drop
640 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: May 15, 1996
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 3594 / % possible obs: 92 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.2→2.35 Å / % possible all: 57
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / % possible obs: 92 % / Observed criterion σ(I): 2
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.35 Å / % possible obs: 57 %

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GDL023

Resolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.174 --
obs0.174 2534 92.3 %
Displacement parametersBiso mean: 24 Å2
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 41 61 588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.03
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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