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- PDB-8oe3: Crystal structure of the non-canonical quadruplex d(GCATGCT) befo... -

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Basic information

Entry
Database: PDB / ID: 8oe3
TitleCrystal structure of the non-canonical quadruplex d(GCATGCT) before soaking
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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: Oxidative damage induce copper(II)-DNA binding
Authors: Lambert, M.C. / Brazier, J.A. / Cardin, C.J. / 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(*GP*CP*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1948
Polymers4,2272
Non-polymers9676
Water90150
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,38716
Polymers8,4544
Non-polymers1,93312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)22.157, 59.156, 45.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-104-

NCO

21B-227-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 2 through 5)
d_2ens_1(chain "B" and resid 2 through 5)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DCDGA
d_21ens_1DCDGB

NCS oper: (Code: givenMatrix: (0.999211025954, -0.0355991900917, 0.0176074778414), (-0.0356690791603, -0.999356912781, 0.00367119446122), (0.017465463148, -0.00429634050502, -0.999838236444)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.999211025954, -0.0355991900917, 0.0176074778414), (-0.0356690791603, -0.999356912781, 0.00367119446122), (0.017465463148, -0.00429634050502, -0.999838236444)
Vector: 0.250181174971, 8.68104231922, 22.8915591378)

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.77 Å3/Da / Density % sol: 30.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 2 ul 40 mM sodium cacodylate, 1 ul 80 mM hexammine (III) cobalt, 1 ul 10% MPD, 2 ul 800 mM potassium chloride, ul 30 mM sodium chloride, 2 ul 1 mM DNA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.08→24.83 Å / Num. obs: 13221 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 9.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 14
Reflection shellResolution: 1.08→1.1 Å / Num. unique obs: 608 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
GDAdata collection
xia2data reduction
DIALSdata scaling
PHENIXphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→24.83 Å / SU ML: 0.1127 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.1739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.185 1169 4.75 %
Rwork0.1638 23455 -
obs0.1649 13176 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.46 Å2
Refinement stepCycle: LAST / Resolution: 1.08→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 280 42 50 372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013413
X-RAY DIFFRACTIONf_angle_d1.7074669
X-RAY DIFFRACTIONf_chiral_restr0.131765
X-RAY DIFFRACTIONf_plane_restr0.017517
X-RAY DIFFRACTIONf_dihedral_angle_d31.9165161
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.506814801215 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.130.23781470.22622810X-RAY DIFFRACTION94.5
1.13-1.190.20851530.17272908X-RAY DIFFRACTION99.51
1.19-1.260.18731270.17612994X-RAY DIFFRACTION99.81
1.26-1.360.221780.15672925X-RAY DIFFRACTION99.77
1.36-1.50.16671400.17532972X-RAY DIFFRACTION99.65
1.5-1.710.1671210.16292962X-RAY DIFFRACTION99.64
1.72-2.160.17031510.16332933X-RAY DIFFRACTION99.52
2.16-24.830.18581520.15332951X-RAY DIFFRACTION99.33

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