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- PDB-8oea: Crystal structure of the Z-DNA duplex d(CGCGCG) soaked in copper(... -

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Basic information

Entry
Database: PDB / ID: 8oea
TitleCrystal structure of the Z-DNA duplex d(CGCGCG) soaked in copper(II) chloride, in preparation to hydrogen peroxide soaking, first collection at room temperature
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLambert, M.C. / Hall, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Structural analysis of peroxide-soaked DNA crystals containing ordered copper binding sites: towards understanding oxidative damage at the atomic scale
Authors: Lambert, M.C. / Hall, J.P.
History
DepositionMar 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,94015
Polymers7,2414
Non-polymers69911
Water82946
1
A: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0028
Polymers3,6202
Non-polymers3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9387
Polymers3,6202
Non-polymers3185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.091, 30.651, 42.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.65 Å3/Da / Density % sol: 25.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, KCl, NaCl and spermine tetrachloride

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.5→18.09 Å / Num. obs: 13568 / % possible obs: 91.7 % / Redundancy: 2.6 % / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1205 / CC1/2: 0.683

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18.09 Å / Cross valid method: FREE R-VALUE / σ(F): 2.27 / Phase error: 24.9725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 734 4.98 %
Rwork0.1786 14019 -
obs0.1845 7645 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.46 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 11 46 537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004602
X-RAY DIFFRACTIONf_angle_d0.6431928
X-RAY DIFFRACTIONf_chiral_restr0.0404104
X-RAY DIFFRACTIONf_plane_restr0.002327
X-RAY DIFFRACTIONf_dihedral_angle_d30.9029263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.620.31671360.22122828X-RAY DIFFRACTION95.25
1.62-1.780.24491260.20362827X-RAY DIFFRACTION95.41
1.78-2.040.26641940.1922741X-RAY DIFFRACTION93.07
2.04-2.560.22471780.19392791X-RAY DIFFRACTION93.91
2.57-18.090.16191000.15492832X-RAY DIFFRACTION96.29

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