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- PDB-8eda: An alternating AT dodecamer benzimidazole (DB1476) complex -

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Basic information

Entry
Database: PDB / ID: 8eda
TitleAn alternating AT dodecamer benzimidazole (DB1476) complex
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3')
KeywordsDNA / SMALL MOLECULE / MINOR GROOVE
Function / homologyChem-WFB / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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
CitationJournal: 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.
History
DepositionSep 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)7,7054
Polymers7,3272
Non-polymers3792
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.743, 39.895, 66.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21(chain C and resid 13 through 24)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 12

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1chain BBA1 - 12
2(chain C and resid 13 through 24)CB13 - 24

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: A self-complementary DNA (5'-CGCGATATCGCG-3') bound by the ligand (DB1476).
Source: (synth.) Homo sapiens (human)
#2: 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
#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.: 118 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, MAGNESIUM CHLORIDE HEXAHYDRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 18, 2022
RadiationMonochromator: double-crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→34.21 Å / Num. obs: 8949 / % possible obs: 99.2 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 21.7
Reflection shellResolution: 1.63→1.69 Å / Num. unique obs: 840 / CC1/2: 1

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Processing

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

1bna


Resolution: 1.63→34.21 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 889 9.97 %
Rwork0.1827 8030 -
obs0.1847 8919 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.09 Å2 / Biso mean: 26.9094 Å2 / Biso min: 14.58 Å2
Refinement stepCycle: final / Resolution: 1.63→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 48 118 652
Biso mean--31.56 35.89 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012574
X-RAY DIFFRACTIONf_angle_d1.402879
X-RAY DIFFRACTIONf_dihedral_angle_d29.178258
X-RAY DIFFRACTIONf_chiral_restr0.07594
X-RAY DIFFRACTIONf_plane_restr0.01829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B232X-RAY DIFFRACTION7.661TORSIONAL
12C232X-RAY DIFFRACTION7.661TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.730.2621390.20091272141197
1.73-1.870.22481460.190913051451100
1.87-2.060.29251480.205213261474100
2.06-2.350.21241490.207913511500100
2.35-2.960.23981490.211613501499100
2.96-34.210.16331580.15721426158499

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