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- PDB-8fdp: The native structure of a dodecamer: 5'-CGCAAATTTGCG-3 -

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Basic information

Entry
Database: PDB / ID: 8fdp
TitleThe native structure of a dodecamer: 5'-CGCAAATTTGCG-3
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*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: 1.88 Å
AuthorsOgbonna, E. / 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 Mol Biol / Year: 1992
Title: Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.
Authors: Edwards, K.J. / Brown, D.G. / Spink, N. / Skelly, J.V. / Neidle, S.
History
DepositionDec 4, 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

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


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
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)24.977, 41.507, 65.449
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_1chain "B"
d_2ens_1chain "C"

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: (0.769370461347, -0.63625107547, -0.0570408815595), (-0.637091318857, -0.770776081865, 0.00434546447809), (-0.0467305536422, 0.0329969784512, -0.998362386496)Vector: 17. ...NCS oper: (Code: given
Matrix: (0.769370461347, -0.63625107547, -0.0570408815595), (-0.637091318857, -0.770776081865, 0.00434546447809), (-0.0467305536422, 0.0329969784512, -0.998362386496)
Vector: 17.2055705627, 47.1936324192, 17.4416754807)

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CGCAAATTTGCG is a self-complementary DNA. Chain B: 5'-CGCAAATTTGCG-3' Chain C: 3'-GCGTTTAAACGC-5'
Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
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: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→23.34 Å / Num. obs: 5921 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01009 / Net I/σ(I): 25
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 577 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata processing
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→23.34 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.3418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 590 9.99 %
Rwork0.2462 5314 -
obs0.2491 5904 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.41 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 28 514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0109544
X-RAY DIFFRACTIONf_angle_d1.2475836
X-RAY DIFFRACTIONf_chiral_restr0.070594
X-RAY DIFFRACTIONf_plane_restr0.010924
X-RAY DIFFRACTIONf_dihedral_angle_d31.9694232
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.886903761 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.070.34191450.29051300X-RAY DIFFRACTION99.86
2.07-2.370.34951430.29521290X-RAY DIFFRACTION99.86
2.37-2.980.34661470.34971336X-RAY DIFFRACTION99.87
2.98-23.340.23691550.20761388X-RAY DIFFRACTION98.85

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