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- PDB-109d: VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDIN... -

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Basic information

Entry
Database: PDB / ID: 109d
TitleVARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX 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
MethodX-RAY DIFFRACTION / 2 Å resolution
AuthorsCzarny, A. / Boykin, D.W. / Wood, A.A. / Nunn, C.M. / Neidle, S. / Zhao, M. / Wilson, W.D.
Citation
Journal: Nucleic Acids Res. / Year: 1995
Title: Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
Authors: Wood, A.A. / Nunn, C.M. / Czarny, A. / Boykin, D.W. / Neidle, S.
#1: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA
Authors: Czarny, A. / Boykin, D.W. / Wood, A.A. / Nunn, C.M. / Neidle, S. / Zhao, M. / Wilson, W.D.
#2: Journal: Biochemistry / Year: 1991
Title: Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G
Authors: Quintana, J.R. / Lipanov, A.A. / Dickerson, R.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 15, 1995 / Release: May 8, 1995
RevisionDateData content typeGroupProviderType
1.0May 8, 1995Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
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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)7,7484
Polyers7,3272
Non-polymers4212
Water1,62190
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)24.590, 40.440, 65.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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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
#2: Chemical ChemComp-IBB / 5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE


Mass: 396.445 Da / Num. of mol.: 1 / Formula: C23H20N6O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 / Density percent sol: 44.88 %
Crystal grow
*PLUS
Temp: 19 ℃ / pH: 7 / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
10.6 mMdodecamer1drop
29.9 %(v/v)MPD1drop
38.6 mMsodium cacodylate1drop
40.3 mMsperine HCl1drop
51.4 mMcompund 21drop
612.9 mM1dropMgCl2
735 %(v/v)MPD1reservoir

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Data collection

SourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionPercent possible obs: 87
Reflection
*PLUS
D resolution high: 2 Å / Number obs: 4365 / Number all: 5026 / Number measured all: 11176 / Percent possible obs: 87 / Rmerge I obs: 0.031

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefineSigma F: 2
Least-squares processR factor R work: 0.197 / R factor obs: 0.197 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 4016
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 486 / Ligand: 37 / Solvent: 84 / Total: 607
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.020
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_deg4.30
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
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å

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