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- PDB-8f20: Structure of an A-tract B-DNA Dodecamer: 5'-CGCAAAAAAGCG-3 -

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Basic information

Entry
Database: PDB / ID: 8f20
TitleStructure of an A-tract B-DNA Dodecamer: 5'-CGCAAAAAAGCG-3
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 / AT sequence / Minor groove
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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
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')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area4530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.662, 41.610, 65.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM 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: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→25.65 Å / Num. obs: 3703 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 65.23 Å2 / CC1/2: 1 / Net I/σ(I): 24.03
Reflection shellResolution: 2.23→2.31 Å / Num. unique obs: 374 / CC1/2: 0.918

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Processing

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

1bna


Resolution: 2.23→25.65 Å / SU ML: 0.4338 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 43.357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2854 370 10.04 %
Rwork0.2519 3314 -
obs0.2551 3684 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.11 Å2
Refinement stepCycle: LAST / Resolution: 2.23→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 5 491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011544
X-RAY DIFFRACTIONf_angle_d1.3248836
X-RAY DIFFRACTIONf_chiral_restr0.059494
X-RAY DIFFRACTIONf_plane_restr0.009524
X-RAY DIFFRACTIONf_dihedral_angle_d33.3483232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.550.45991200.33041083X-RAY DIFFRACTION100
2.55-3.210.39071220.38741092X-RAY DIFFRACTION99.35
3.22-25.650.24271280.21141139X-RAY DIFFRACTION98.83

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