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- PDB-8baf: Non-canonical quadruplex containing the oxidation product 8-oxoguanine -

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Basic information

Entry
Database: PDB / ID: 8baf
TitleNon-canonical quadruplex containing the oxidation product 8-oxoguanine
ComponentsDNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: 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(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9036
Polymers4,2592
Non-polymers6444
Water84747
1
A: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,54810
Polymers4,2592
Non-polymers1,2898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
2
B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')

B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)4,2592
Polymers4,2592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)22.035, 58.846, 45.488
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-102-

NCO

21A-102-

NCO

31A-102-

NCO

41B-129-

HOH

51B-132-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 5)
d_2ens_1(chain "B" and resid 1 through 5)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_18OGDGA
d_21ens_18OGDGB

NCS oper: (Code: givenMatrix: (0.998957069471, -0.0350448733463, -0.0292682456986), (-0.0356383850152, -0.99916442527, -0.0200089177104), (-0.0285425799052, 0.0210311228082, -0.999371308877)Vector: - ...NCS oper: (Code: given
Matrix: (0.998957069471, -0.0350448733463, -0.0292682456986), (-0.0356383850152, -0.99916442527, -0.0200089177104), (-0.0285425799052, 0.0210311228082, -0.999371308877)
Vector: -0.822621414885, -8.91881069764, -22.6150054217)

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Components

#1: DNA chain DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')


Mass: 2129.410 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.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.73 Å3/Da / Density % sol: 28.95 %
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: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→18.79 Å / Num. obs: 4151 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 6.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Rrim(I) all: 0.086 / Net I/σ(I): 13.6
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 301 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF5

1mf5


Resolution: 1.6→18.79 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.6523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1969 326 4.39 %
Rwork0.1861 7101 -
obs0.1866 4128 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 282 28 47 357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0216338
X-RAY DIFFRACTIONf_angle_d2.0374542
X-RAY DIFFRACTIONf_chiral_restr0.099154
X-RAY DIFFRACTIONf_plane_restr0.011914
X-RAY DIFFRACTIONf_dihedral_angle_d31.3623120
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.50019490718 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-2.020.21381570.21083551X-RAY DIFFRACTION97.89
2.02-18.790.18851690.17233550X-RAY DIFFRACTION98.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.91117540058-0.2321890161911.652825482271.21420337783-2.589107106578.635825261580.3837859954690.385020423154-0.52935754458-0.475158626698-0.01254866045790.1447117395981.57194064652-0.6142804949171.003499984860.1486118583540.02240295505470.000604007825350.120337963328-0.02389874474950.111283214166-2.21288354582-10.897189618-16.2581275408
22.38568191298-0.477336534744-1.385197555590.626262556645-0.6891499974276.680363963730.309144073614-0.2143422312840.1952899282340.25313393323-0.04689040605440.0181748840284-1.09733172984-0.3006159745220.880887140568-0.0266646472656-0.0271280633523-0.0101020663150.0559135013753-0.009159867498580.0531387002507-2.150805871812.3216021593-6.39452191348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 7 )AA2 - 7
2X-RAY DIFFRACTION2chain 'B' and (resid 2 through 7 )BB2 - 7

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