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- PDB-8bag: Copper(II) bound to a non-canonical quadruplex containing the dam... -

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Basic information

Entry
Database: PDB / ID: 8bag
TitleCopper(II) bound to a non-canonical quadruplex containing the damaged base 8-oxoguanine
ComponentsDNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / COBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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)5,0308
Polymers4,2592
Non-polymers7726
Water91951
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)5,67512
Polymers4,2592
Non-polymers1,41610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,3864
Polymers4,2592
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)21.990, 58.870, 45.460
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

21B-219-

HOH

31B-225-

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: (0.99886184781, -0.0401425817238, 0.0257600877856), (-0.0399546431106, -0.999171286283, -0.00776963073116), (0.0260506330841, 0.00673155259496, -0.999637959821)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.99886184781, -0.0401425817238, 0.0257600877856), (-0.0399546431106, -0.999171286283, -0.00776963073116), (0.0260506330841, 0.00673155259496, -0.999637959821)
Vector: 0.169549702879, 8.69758057536, 22.6863258865)

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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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.73 Å3/Da / Density % sol: 28.79 %
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: 0.97624 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.13→29.43 Å / Num. obs: 11191 / % possible obs: 97.89 % / Redundancy: 1 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.964 / Num. unique obs: 495 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
xia2data scaling
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF5

1mf5


Resolution: 1.13→29.43 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1724 995 4.77 %
Rwork0.1518 19865 -
obs0.1528 11162 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.13→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 282 30 51 363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166344
X-RAY DIFFRACTIONf_angle_d1.7557557
X-RAY DIFFRACTIONf_chiral_restr0.078654
X-RAY DIFFRACTIONf_plane_restr0.011714
X-RAY DIFFRACTIONf_dihedral_angle_d31.0925120
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.488060752785 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.190.26621150.24222647X-RAY DIFFRACTION91.46
1.19-1.260.20181090.18232874X-RAY DIFFRACTION96.91
1.26-1.360.19321650.16242836X-RAY DIFFRACTION98.3
1.36-1.50.18481580.15882847X-RAY DIFFRACTION98.62
1.5-1.720.17791470.14982871X-RAY DIFFRACTION99.08
1.72-2.160.18811480.14932890X-RAY DIFFRACTION99.7
2.16-29.430.15261530.14022900X-RAY DIFFRACTION99.64

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