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- PDB-8bae: Copper(II) bound to a non-canonical quadruplex -

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Basic information

Entry
Database: PDB / ID: 8bae
TitleCopper(II) bound to a non-canonical quadruplex
ComponentsDNA (5'-D(*GP*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 / MOLECULAR REPLACEMENT / Resolution: 1.2 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

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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)4,9988
Polymers4,2272
Non-polymers7726
Water1,22568
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)9,99716
Polymers8,4544
Non-polymers1,54312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)21.954, 58.867, 45.601
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
11B-102-

NCO

21B-102-

NCO

31B-102-

NCO

41A-230-

HOH

51A-232-

HOH

61B-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: (0.999183624594, -0.0364997351989, 0.017316283486), (-0.036485103234, -0.999333523431, -0.00116025402644), (0.0173470915535, 0.000527520432968, -0.999849388727)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.999183624594, -0.0364997351989, 0.017316283486), (-0.036485103234, -0.999333523431, -0.00116025402644), (0.0173470915535, 0.000527520432968, -0.999849388727)
Vector: 0.280410821714, 8.70812634757, 22.8190234711)

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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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.74 Å3/Da / Density % sol: 29.43 %
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: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→20.57 Å / Num. obs: 9598 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 7.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 473 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
CrysalisPro42.60adata collection
CrysalisPro42.60adata reduction
CrysalisPro42.60adata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF5

1mf5


Resolution: 1.2→20.57 Å / SU ML: 0.0982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1819 --
Rwork0.1349 16923 -
obs0.1372 9566 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.29 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 280 30 68 378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006407
X-RAY DIFFRACTIONf_angle_d0.8658654
X-RAY DIFFRACTIONf_chiral_restr0.053665
X-RAY DIFFRACTIONf_plane_restr0.007317
X-RAY DIFFRACTIONf_dihedral_angle_d31.9091161
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.495885594879 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.280.23321420.18932786X-RAY DIFFRACTION98.72
1.28-1.370.2121570.15682821X-RAY DIFFRACTION99.87
1.37-1.510.19941380.15292831X-RAY DIFFRACTION100
1.51-1.730.16581330.13292854X-RAY DIFFRACTION99.77
1.73-2.180.17331440.13152822X-RAY DIFFRACTION99.87
2.18-20.570.16831650.11562809X-RAY DIFFRACTION99.7

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