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- PDB-444d: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', BENZIMIDAZOLE DERIV... -

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Basic information

Entry
Database: PDB / ID: 444d
Title5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', BENZIMIDAZOLE DERIVATIVE COMPLEX
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / MINOR GROOVE BINDING
Function / homologyChem-IB / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsClark, G.R. / Squire, C.J. / Martin, R.F. / White, J.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design.
Authors: Squire, C.J. / Baker, L.J. / Clark, G.R. / Martin, R.F. / White, J.
#1: Journal: Nucleic Acids Res. / Year: 2000
Title: Intermolecular interactions and water structure in a condensed phase B-DNA crystal
Authors: Clark, G.R. / Squire, C.J. / Baker, L.J. / Martin, R.F. / White, J.
History
DepositionJan 14, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Dec 27, 2023Group: 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)7,8923
Polymers7,3272
Non-polymers5651
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.37, 40.48, 66.08
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
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-IB / 2'-(3-IODO-4-METHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE


Mass: 565.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26IN6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE11
3SODIUM CACODYLATE11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.57 mMDNA1drop
20.71 mMligand1drop
38.6 mM1dropMgCl2
40.95 mMspermine1drop
53.8 %1drop
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 0.7107
DetectorType: BRUKER SMART / Detector: CCD / Date: Nov 7, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. all: 2916 / Num. obs: 2916 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Redundancy: 7.05 % / Rmerge(I) obs: 0.118
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.521 / % possible all: 41.8
Reflection shell
*PLUS
% possible obs: 41.8 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SAINTdata reduction
SAINTdata scaling
SADABSdata scaling
X-PLORphasing
RefinementResolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -10 %RANDOM
Rwork0.205 ---
obs0.205 2513 --
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 68 9 563
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_deg1.066
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

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