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- PDB-8f1v: A benzimidazole (DB1476) sequence-specific recognition of 5'-CGCA... -

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Basic information

Entry
Database: PDB / ID: 8f1v
TitleA benzimidazole (DB1476) sequence-specific recognition of 5'-CGCAAAAAAGCG-3' in B-orientation
Components
  • DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / Minor groove binder / Minor groove / sequence recognition
Function / homologyChem-WFB / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOgbonna, E.N. / Wilson, W.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
Citation
Journal: Acs Bio Med Chem Au / Year: 2023
Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D.
#1: Journal: J Org Chem / Year: 2014
Title: Design and synthesis of heterocyclic cations for specific DNA recognition: from AT-rich to mixed-base-pair DNA sequences.
Authors: Chai, Y. / Paul, A. / Rettig, M. / Wilson, W.D. / Boykin, D.W.
History
DepositionNov 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7044
Polymers7,3252
Non-polymers3792
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, 5'-CGCAAAAAAGCG-3' l l l l l l l l l l l l DB1476 l l l l l l l l l l l l 3'-GCGTTTTTTCGC-5
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-11 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.030, 41.458, 64.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*AP*GP*CP*G)-3')


Mass: 3689.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*TP*TP*TP*TP*TP*GP*CP*G)-3')


Mass: 3635.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-WFB / 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)


Mass: 354.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N6
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, SODIUM CACOCYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM HEXAHYDRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25.33 Å / Num. obs: 4201 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 9.71
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 403 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC3.27data processing
XDSdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 2.1→25.33 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 43.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3251 421 10.06 %
Rwork0.2772 3765 -
obs0.2823 4186 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.97 Å2 / Biso mean: 47.1386 Å2 / Biso min: 39.02 Å2
Refinement stepCycle: final / Resolution: 2.1→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 48 14 548
Biso mean--50.42 43.61 -
Num. residues----24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.40.46141360.401512131349100
2.4-3.030.39971370.372312441381100
3.03-25.330.28841480.23371308145699

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