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- PDB-8f2w: Structure of a B-Form Dodecamer: 5'-CGCGAATTCGCG-3 -

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Basic information

Entry
Database: PDB / ID: 8f2w
TitleStructure of a B-Form Dodecamer: 5'-CGCGAATTCGCG-3
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*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: 1.3 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: PNAS Biochemistry / Year: 1988
Title: Structure of an alternating B-DNA helix and its relationship to A-tract DNA
Authors: Yoon, C. / Prive, G.G. / Goodsell, D.S. / Dickerson, R.E. / Boykin, D.W.
History
DepositionNov 8, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3513
Polymers7,3272
Non-polymers241
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.580, 40.104, 66.099
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and ((resid 1 and (name O5" or name...
d_2ens_1(chain "C" and ((resid 13 and (name O5" or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DCDGA
d_21ens_1DCDGB

NCS oper: (Code: givenMatrix: (0.705840847997, -0.705948755209, -0.0585239465422), (-0.707291258126, -0.706914847883, -0.00323635923381), (-0.0390867429949, 0.0436778303264, -0.998280758935)Vector: ...NCS oper: (Code: given
Matrix: (0.705840847997, -0.705948755209, -0.0585239465422), (-0.707291258126, -0.706914847883, -0.00323635923381), (-0.0390867429949, 0.0436778303264, -0.998280758935)
Vector: 19.4694753062, 46.391168871, 17.168932783)

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Self-complementary native DNA dodecamer (5'-CGCGAATTCGCG-3')
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2021
RadiationMonochromator: double crystal - LN cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→34.3 Å / Num. obs: 16736 / % possible obs: 95.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.981 / Net I/σ(I): 16.74
Reflection shellResolution: 1.3→1.35 Å / Num. unique obs: 1649 / CC1/2: 0.8

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Processing

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

1bna


Resolution: 1.3→34.29 Å / SU ML: 0.1603 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 1664 10.05 %
Rwork0.1865 14885 -
obs0.1894 16549 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.24 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 135 622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114544
X-RAY DIFFRACTIONf_angle_d1.4438836
X-RAY DIFFRACTIONf_chiral_restr0.073494
X-RAY DIFFRACTIONf_plane_restr0.021724
X-RAY DIFFRACTIONf_dihedral_angle_d31.0051232
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.77594464493 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.32821380.26691247X-RAY DIFFRACTION96.79
1.34-1.380.30781370.23981226X-RAY DIFFRACTION96.74
1.38-1.430.25511390.22421248X-RAY DIFFRACTION97.33
1.43-1.490.25591360.21631228X-RAY DIFFRACTION95.38
1.49-1.560.29121320.21591186X-RAY DIFFRACTION93.87
1.56-1.640.19281280.1781127X-RAY DIFFRACTION87.27
1.64-1.740.19361330.14921151X-RAY DIFFRACTION89.35
1.74-1.870.19921370.16251232X-RAY DIFFRACTION95.4
1.87-2.060.19241410.17161259X-RAY DIFFRACTION96.09
2.06-2.360.23221450.18181302X-RAY DIFFRACTION98.64
2.36-2.980.23691470.20171330X-RAY DIFFRACTION99.46
2.98-34.290.19121510.18151349X-RAY DIFFRACTION95.72

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