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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
Function / homologyChem-IBB / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
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.
History
DepositionFeb 15, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)7,7484
Polymers7,3272
Non-polymers4212
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-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-IBB / 5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common 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

Diffraction 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
Reflection% possible obs: 87 %
Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 5026 / Num. obs: 4365 / % possible obs: 87 % / Num. measured all: 11176 / Rmerge(I) obs: 0.031

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 4016
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 37 84 607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg4.3
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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