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- PDB-8oe7: Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordere... -

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Basic information

Entry
Database: PDB / ID: 8oe7
TitleCrystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for 5 minutes
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / HYDROGEN PEROXIDE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)15,99135
Polymers14,4828
Non-polymers1,50927
Water2,882160
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)4,0069
Polymers3,6202
Non-polymers3867
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)4,04010
Polymers3,6202
Non-polymers4208
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)3,9387
Polymers3,6202
Non-polymers3185
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)4,0069
Polymers3,6202
Non-polymers3867
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.282, 30.737, 42.557
Angle α, β, γ (deg.)90.010, 89.950, 90.010
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(0.20783296712, 0.977649224815, 0.0317403685725), (0.976069713964, -0.20940111543, 0.058643723785), (0.0639794596819, 0.0187927133565, -0.99777425436)2.78400100182, -4.23879961728, 15.5801992146
2given(0.99999730743, -0.00199945691912, -0.00117783877492), (-0.0019990536544, -0.99999794291, 0.000343454682738), (-0.00117852307484, -0.000341099195055, -0.999999247367)9.15228909454, -14.5918393374, 21.3860260671
3given(0.212639361181, 0.976616602301, 0.0316940717862), (-0.97487600649, 0.214239290212, -0.0609778525269), (-0.0663420985938, -0.0179314985248, 0.997635798934)11.9131665242, -10.3489871346, 5.8084888209
4given(-0.999998508045, -0.00152478955149, 0.000811741583535), (-0.0015230398776, 0.9999965252, 0.00215172894453), (-0.000815019696707, 0.00215048941945, -0.999997355566)18.5593769176, 15.3490860782, 42.6640967925
5given(-0.213762230882, -0.976377097156, -0.0315194035065), (0.974624046845, -0.215350565556, 0.0610909258935), (-0.0664355022576, -0.017660635994, 0.997634414992)15.787093325, 11.1309587888, 27.0803437903
6given(-0.999998172705, 0.00186408947445, -0.000423978438295), (-0.00186404533116, -0.999998257207, -0.000104488157719), (-0.000424172474663, -0.000103697651759, 0.999999904662)9.41667510734, 0.775437974894, 21.275234506
7given(-0.206369749578, -0.977951575132, -0.0319725375302), (-0.976351845881, 0.207963131548, -0.0590627544422), (0.0644096227667, 0.0190276801915, -0.997742124941)6.61868623436, 5.01677409292, 36.8454471634

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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.: 20 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 25.52 %
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: 1.25→30.74 Å / Num. obs: 24395 / % possible obs: 95.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.55 Å2 / CC1/2: 1 / Net I/σ(I): 19.7
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 1129 / CC1/2: 0.94

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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: 1.25→24.92 Å / SU ML: 0.1506 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.0122
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2548 5.29 %
Rwork0.1994 45627 -
obs0.2012 24320 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.97 Å2
Refinement stepCycle: LAST / Resolution: 1.25→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 960 34 160 1154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831233
X-RAY DIFFRACTIONf_angle_d0.99641892
X-RAY DIFFRACTIONf_chiral_restr0.0546212
X-RAY DIFFRACTIONf_plane_restr0.008955
X-RAY DIFFRACTIONf_dihedral_angle_d30.3744539
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.718565602201
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.0649358996204
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.716147057147
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.0398694611291
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.726191687607
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.0415240148064
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.716148679459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.29391560.20432363X-RAY DIFFRACTION89.39
1.27-1.30.20711180.18632643X-RAY DIFFRACTION92.9
1.3-1.330.2871550.20382450X-RAY DIFFRACTION91.79
1.33-1.360.36062110.1922426X-RAY DIFFRACTION92.33
1.36-1.390.28281810.20832459X-RAY DIFFRACTION92.96
1.39-1.430.21711340.20162411X-RAY DIFFRACTION92.28
1.43-1.470.2521500.19452503X-RAY DIFFRACTION93.55
1.47-1.520.23141330.18152620X-RAY DIFFRACTION94.41
1.52-1.580.31011250.18192462X-RAY DIFFRACTION93.73
1.58-1.640.19561080.18072681X-RAY DIFFRACTION93.72
1.64-1.710.20961310.17072494X-RAY DIFFRACTION93.68
1.71-1.80.20561270.17882552X-RAY DIFFRACTION93.61
1.8-1.920.1869750.212600X-RAY DIFFRACTION94.93
1.92-2.060.28931150.20242629X-RAY DIFFRACTION96.08
2.06-2.270.28571720.23992570X-RAY DIFFRACTION96.69
2.27-2.60.24421230.22562642X-RAY DIFFRACTION97.29
2.6-3.270.22961540.23132570X-RAY DIFFRACTION95.65
3.28-24.920.18241800.17072552X-RAY DIFFRACTION96.06

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