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- PDB-8oex: Crystal structure of the native Z-DNA duplex d(CGCGCG) before soa... -

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Basic information

Entry
Database: PDB / ID: 8oex
TitleCrystal structure of the native Z-DNA duplex d(CGCGCG) before soaking of CuCl2
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologySPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.07 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 13, 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-1 kcal/mol
Surface area2470 Å2
Unit cell
Length a, b, c (Å)18.283, 30.764, 42.477
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 2 or resid 4 or resid 6))
d_2ens_1(chain "B" and (resid 2 or resid 4 or resid 6))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DGDGA
d_21ens_1DGDGC

NCS oper: (Code: givenMatrix: (0.200254449754, 0.978359251498, 0.0520704365433), (0.978406403649, -0.202474560624, 0.0415326570081), (0.0511767979838, 0.0426289491788, -0.997779388462)Vector: 3. ...NCS oper: (Code: given
Matrix: (0.200254449754, 0.978359251498, 0.0520704365433), (0.978406403649, -0.202474560624, 0.0415326570081), (0.0511767979838, 0.0426289491788, -0.997779388462)
Vector: 3.32370630606, -3.93802815305, -5.76141024713)

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 25.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, pH 6.0, KCl, NaCl and spermine tetrachloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.07→18.28 Å / Num. obs: 10952 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 4.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.077 / Rrim(I) all: 0.199 / Net I/σ(I): 11.4
Reflection shellResolution: 1.07→1.09 Å / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 480 / CC1/2: 0.868 / Rpim(I) all: 0.241 / Rrim(I) all: 0.606 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→17.48 Å / SU ML: 0.0553 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 10.9522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1252 548 5.03 %
Rwork0.1053 10346 -
obs0.1063 10894 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.27 Å2
Refinement stepCycle: LAST / Resolution: 1.07→17.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 88 342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011343
X-RAY DIFFRACTIONf_angle_d1.3964522
X-RAY DIFFRACTIONf_chiral_restr0.058357
X-RAY DIFFRACTIONf_plane_restr0.021115
X-RAY DIFFRACTIONf_dihedral_angle_d29.8572158
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.870690915951 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.180.15851360.12722493X-RAY DIFFRACTION98.21
1.18-1.350.12891380.10952541X-RAY DIFFRACTION99.96
1.35-1.710.11581270.10492608X-RAY DIFFRACTION99.82

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