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- PDB-8oec: Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordere... -

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Basic information

Entry
Database: PDB / ID: 8oec
TitleCrystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for another 30 minutes, third collection at room temperature
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / SPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8864
Polymers3,6202
Non-polymers2662
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-6 kcal/mol
Surface area2520 Å2
Unit cell
Length a, b, c (Å)18.355, 30.778, 43.104
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 "A" and (resid 1 through 2 or resid 4 through 6))
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4 through 6))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DCDGA
d_21ens_1DCDGC

NCS oper: (Code: givenMatrix: (0.223088265613, 0.973125932262, 0.0570749130893), (0.972127118702, -0.226426787544, 0.0608257755157), (0.0721144287245, 0.0419145540473, -0.996515267986)Vector: 3. ...NCS oper: (Code: given
Matrix: (0.223088265613, 0.973125932262, 0.0570749130893), (0.972127118702, -0.226426787544, 0.0608257755157), (0.0721144287245, 0.0419145540473, -0.996515267986)
Vector: 3.33880447589, -3.83968745442, -5.9498604081)

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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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.68 Å3/Da / Density % sol: 26.85 %
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: 2.1→17.65 Å / Num. obs: 1612 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.25 Å / Num. unique obs: 285 / CC1/2: 0.982

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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: 2.1→17.65 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.5244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 142 5.23 %
Rwork0.1467 2572 -
obs0.1492 1586 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 15 31 286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041303
X-RAY DIFFRACTIONf_angle_d0.6671458
X-RAY DIFFRACTIONf_chiral_restr0.040350
X-RAY DIFFRACTIONf_plane_restr0.003113
X-RAY DIFFRACTIONf_dihedral_angle_d29.7255136
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.513024023792 Å
LS refinement shellResolution: 2.1→17.65 Å
RfactorNum. reflection% reflection
Rfree0.188 142 -
Rwork0.1467 2572 -
obs--98.58 %

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