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- PDB-8f2y: Structure of an alternating AT dodecamer: 5'-CGCGATATCGCG-3 -

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Basic information

Entry
Database: PDB / ID: 8f2y
TitleStructure of an alternating AT dodecamer: 5'-CGCGATATCGCG-3
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*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: 1.78 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: Biochemistry / Year: 1989
Title: Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.
Authors: Coll, M. / Aymami, J. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H.
History
DepositionNov 9, 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*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)7,3513
Polymers7,3272
Non-polymers241
Water1,71195
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)25.486, 40.362, 66.692
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: (0.710580337659, -0.702920432949, -0.0312801642587), (-0.703505296372, -0.710554893073, -0.0138579185359), (-0.0124852596732, 0.0318529256598, -0.999414583353)Vector: 19. ...NCS oper: (Code: given
Matrix: (0.710580337659, -0.702920432949, -0.0312801642587), (-0.703505296372, -0.710554893073, -0.0138579185359), (-0.0124852596732, 0.0318529256598, -0.999414583353)
Vector: 19.0185089322, 46.3698235671, 17.9877886471)

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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: Native alternating AT DNA dodecamer (5'-CGCGATATCGCG-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.: 95 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLROIDE, 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: 1.78→25.71 Å / Num. obs: 7017 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 11.2
Reflection shellResolution: 1.78→1.84 Å / Rmerge(I) obs: 0.1557 / Num. unique obs: 692 / CC1/2: 0.955 / Rpim(I) all: 0.1557 / Rrim(I) all: 0.2202

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.19.2_4158data processing
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 1.78→25.71 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.3698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 700 9.99 %
Rwork0.2086 6304 -
obs0.2104 7004 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.55 Å2
Refinement stepCycle: LAST / Resolution: 1.78→25.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 95 582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116544
X-RAY DIFFRACTIONf_angle_d1.4004836
X-RAY DIFFRACTIONf_chiral_restr0.070494
X-RAY DIFFRACTIONf_plane_restr0.015424
X-RAY DIFFRACTIONf_dihedral_angle_d30.5431232
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.05791582552 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.920.33351380.25831239X-RAY DIFFRACTION99.78
1.92-2.110.27731360.24191230X-RAY DIFFRACTION99.78
2.11-2.420.29141370.2361238X-RAY DIFFRACTION100
2.42-3.040.23171410.23551266X-RAY DIFFRACTION99.93
3.04-25.710.17771480.17391331X-RAY DIFFRACTION98.8

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