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- PDB-453d: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-BENZIMIDAZOLE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 453d
Title5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-BENZIMIDAZOLE COMPLEX
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / MINOR GROOVE BINDING
Function / homologyChem-E96 / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNeidle, S.
CitationJournal: J.Chem.Soc.,Chem.Commun. / Year: 1999
Title: Symmetric bis-benzimidazoles, a new class of sequence-selective DNA-binding molecules
Authors: Neidle, S. / Mann, J. / Rayner, E.J. / Baron, A. / Opoku-Boahen, Y. / Simpson, I.J. / Smith, N.J. / Fox, K.R. / Hartley, J.A. / Kelland, L.R.
History
DepositionFeb 18, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0May 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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)7,7453
Polymers7,3272
Non-polymers4181
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.460, 39.960, 65.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-E96 / 4-{[4-HYDROXY-PHENYL]-1H-BENZIMIDAZOLE-5-YL}-BENZIMIDAZOLE-2-YL-[4-HYDROXY-BENZENE]


Mass: 418.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H18N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MPD11
3MGCL211
4KCL11
5SPERMINE11
6MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 1997 / Details: YALE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. all: 6380 / Num. obs: 6157 / % possible obs: 98 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→8 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.251 319 5 %
Rwork0.234 --
all0.232 6465 -
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 32 174 692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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