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- PDB-8oe8: Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordere... -

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Basic information

Entry
Database: PDB / ID: 8oe8
TitleCrystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for an hour
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / HYDROGEN PEROXIDE / SPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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')
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,02424
Polymers14,4828
Non-polymers1,54216
Water2,702150
1
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)3,9505
Polymers3,6202
Non-polymers3293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)4,0477
Polymers3,6202
Non-polymers4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0136
Polymers3,6202
Non-polymers3934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0136
Polymers3,6202
Non-polymers3934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.346, 30.665, 42.859
Angle α, β, γ (deg.)89.980, 90.060, 89.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 2 or resid 4 or resid 6))
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4 or resid 6))
d_3ens_1(chain "C" and (resid 1 through 2 or resid 4 or resid 6))
d_4ens_1(chain "D" and (resid 1 through 2 or resid 4 or resid 6))
d_5ens_1(chain "E" and (resid 1 through 2 or resid 4 or resid 6))
d_6ens_1(chain "F" and (resid 1 through 2 or resid 4 or resid 6))
d_7ens_1(chain "G" and (resid 1 through 2 or resid 4 or resid 6))
d_8ens_1(chain "H" and (resid 1 through 2 or resid 4 or resid 6))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DCDGA
d_21ens_1DCDGB
d_31ens_1DCDGC
d_41ens_1DCDGD
d_51ens_1DCDGE
d_61ens_1DCDGF
d_71ens_1DCDGG
d_81ens_1DCDGH

NCS oper:
IDCodeMatrixVector
1given(0.208802025793, 0.976999975809, 0.0432754121278), (0.97579200019, -0.211078960087, 0.0572332505986), (0.0650514134395, 0.0302773822916, -0.997422475048)11.8816422446, -12.0375237144, -48.6334603331
2given(-0.999996391398, -0.00266787164409, -0.000315677419302), (0.00266821817978, -0.999995832576, -0.00110247135401), (-0.000312734851677, -0.00110330967186, 0.999999342452)11.4266315989, -13.5490825403, 21.4241661224
3given(-0.209682901599, -0.976848494277, -0.0424275854351), (-0.975588619993, 0.211914686058, -0.057610852902), (0.065268103359, 0.0293118587242, -0.997437160738)-0.395970503399, -1.48805105774, -27.2032881712
4given(0.999996229089, 0.00274623412449, 2.47931434122E-6), (0.00274623021559, -0.999992263086, -0.0028163784174), (-5.25513935837E-6, 0.00281637460586, -0.999996033995)-9.1552082912, 1.7334047098, -42.8708793811
5given(0.210266870698, 0.976690134402, 0.0431766655556), (-0.975506020931, 0.212521502172, -0.0567680741452), (-0.0646207877893, -0.0301826519071, 0.997453337911)2.69254178328, 13.8672475885, 5.74246561838
6given(-0.999995962066, -0.00200129347836, 0.00201759187396), (-0.00199796915469, 0.999996645541, 0.0016483403431), (-0.00202088391881, 0.00164430260088, -0.999996606143)2.37965523499, 15.3696993536, -64.2970034309
7given(-0.207632591137, -0.977182178904, -0.0447626666976), (0.976072460469, -0.209983774429, 0.0564744755718), (-0.0645852847984, -0.0319656645246, 0.997400088871)-9.58325956477, 3.27552947709, -15.692402041

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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.: 8 / 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: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.66 Å3/Da / Density % sol: 26.13 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→42.86 Å / Num. obs: 21952 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.9
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1072 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
GDAdata collection
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→21.43 Å / SU ML: 0.173 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.1081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1973 4.53 %
Rwork0.1691 41567 -
obs0.171 21922 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 960 37 150 1147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791357
X-RAY DIFFRACTIONf_angle_d0.94912088
X-RAY DIFFRACTIONf_chiral_restr0.0519232
X-RAY DIFFRACTIONf_plane_restr0.008360
X-RAY DIFFRACTIONf_dihedral_angle_d30.2476616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.670137558746
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.0242511711185
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.663404656821
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.0303386445768
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.665041445486
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.0267699882007
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.668654316454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.30871460.27652870X-RAY DIFFRACTION89.6
1.33-1.370.4425900.24862922X-RAY DIFFRACTION92.68
1.37-1.410.32041300.23662995X-RAY DIFFRACTION93.51
1.41-1.450.23021060.19852869X-RAY DIFFRACTION92.85
1.45-1.510.27251520.19752932X-RAY DIFFRACTION93.85
1.51-1.570.26331360.16522958X-RAY DIFFRACTION93.99
1.57-1.640.18961810.17862980X-RAY DIFFRACTION95.1
1.64-1.720.17171630.14322890X-RAY DIFFRACTION94.4
1.72-1.830.23161550.17073007X-RAY DIFFRACTION95.07
1.83-1.970.21971740.1482892X-RAY DIFFRACTION95.22
1.97-2.170.24441400.17933039X-RAY DIFFRACTION96.74
2.17-2.490.27531160.17143079X-RAY DIFFRACTION97.41
2.49-3.130.30791270.18163111X-RAY DIFFRACTION97.18
3.13-21.430.13111570.13843023X-RAY DIFFRACTION96.95

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