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- PDB-458d: DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG BY A NO... -

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Basic information

Entry
Database: PDB / ID: 458d
TitleDNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG BY A NON-SELF-COMPLEMENTARY AT-RICH SEQUENCE
Components
  • DNA (5'-D(*CP*GP*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsAymami, J. / Nunn, C.M. / Neidle, S.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand.
Authors: Aymami, J. / Nunn, C.M. / Neidle, S.
History
DepositionMar 10, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 28, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4042
Polymers7,4042
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.190, 40.580, 66.010
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*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3')


Mass: 3732.286 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3')


Mass: 3671.418 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 13 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
175 mM1dropMgCl2
215 mMspermine1drop
33 mMduplex1drop
425 %(w/v)MPD1drop
540 mMsodium cacodylate1drop
635 %(w/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: DOUBLE FOCUSSING MIRROR SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 3508 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.303 210 10 %RANDOM
all0.207 2756 --
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 105 592

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