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- PDB-459d: DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG -

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Basic information

Entry
Database: PDB / ID: 459d
TitleDNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG
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 / MINOR GROOVE BINDING / B-DNA / COMPLEXED WITH TRIS-BENZIMIDAZOLE / DEOXYRIBONUCLEIC ACID
Function / homologyChem-TBZ / DNA / 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 1.1Apr 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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*(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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9453
Polymers7,4042
Non-polymers5421
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.500, 40.420, 65.550
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
Details: COMPLEXED WITH 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2', 5''- TRI-BENZIMIDAZOLE
#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
Details: COMPLEXED WITH 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2', 5''- TRI-BENZIMIDAZOLE
#3: Chemical ChemComp-TBZ / 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE / TRIBIZ / TRIS(BENZIMIDAZOLE) DERIVATIVE


Mass: 541.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29N8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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 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
430 %(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: GRAPHITE / 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: 3281 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 223 10 %RANDOM
obs0.209 ---
all-2695 --
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 42 112 640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.042
X-RAY DIFFRACTIONs_angle_d0.018
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
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.285 / Rfactor Rfree: 0.361
Solvent computation
*PLUS
Displacement parameters
*PLUS

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