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- PDB-6iyq: Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6... -

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Basic information

Entry
Database: PDB / ID: 6iyq
TitleCrystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')
KeywordsDNA / 6-thioguanine / disulfide
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsKondo, J. / Ono, A. / Atsugi, T.
CitationJournal: Rsc Adv / Year: 2019
Title: Crystal structure of a DNA duplex cross-linked by 6-thioguanine-6-thioguanine disulfides: reversible formation and cleavage catalyzed by Cu(II) ion and glutathione
Authors: Ono, A. / Atsugi, T. / Goto, M. / Saneyoshi, H. / Tomori, T. / Seio, K. / Dairaku, T. / Kondo, J.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6032
Polymers7,6032
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint10 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.254, 46.522, 76.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*(S6G)P*(S6G)P*(BRU)P*CP*GP*CP*G)-3')


Mass: 3801.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MOPS (pH 7), spermine, ammonium nitrate, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.91942 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91942 Å / Relative weight: 1
ReflectionResolution: 2.007→39.69 Å / Num. obs: 5619 / % possible obs: 99.8 % / Redundancy: 6.226 % / Biso Wilson estimate: 47.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Χ2: 1.119 / Net I/σ(I): 19.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.01-2.066.650.2875.244000.9780.31298.8
2.06-2.126.6350.2286.093950.9860.24899.7
2.12-2.186.6280.1777.993900.9920.193100
2.18-2.246.540.1798.443670.9920.195100
2.24-2.326.2080.13310.753650.9940.146100
2.32-2.46.310.10414.033580.9960.113100
2.4-2.496.2070.09415.43430.9950.103100
2.49-2.596.7330.08718.683260.9960.094100
2.59-2.716.6610.07520.23190.9970.082100
2.71-2.846.3460.06823.053010.9980.075100
2.84-2.996.1910.05126.452880.9980.056100
2.99-3.176.0430.04292790.9990.045100
3.17-3.395.510.03529.926110.03999.6
3.39-3.665.6180.03931.782380.9990.043100
3.66-4.016.1050.0433.422280.9990.04499.6
4.01-4.496.0520.03934.082100.9990.043100
4.49-5.185.7530.04433.561860.9990.048100
5.18-6.355.1370.04331.891610.9970.047100
6.35-8.985.0390.04431.361270.9980.048100
8.98-39.695.0910.03531.96770.9980.03995.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVEphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.01→39.69 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 39.96
RfactorNum. reflection% reflection
Rfree0.2819 557 9.95 %
Rwork0.2469 --
obs0.2506 5598 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.81 Å2 / Biso mean: 46.4802 Å2 / Biso min: 31.22 Å2
Refinement stepCycle: final / Resolution: 2.01→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 2 494
Biso mean---44.67 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013554
X-RAY DIFFRACTIONf_angle_d1.387850
X-RAY DIFFRACTIONf_chiral_restr0.05488
X-RAY DIFFRACTIONf_plane_restr0.0124
X-RAY DIFFRACTIONf_dihedral_angle_d36.422196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0072-2.20910.42781360.35941220135699
2.2091-2.52870.40041390.338712461385100
2.5287-3.18570.34741400.294912551395100
3.1857-39.6980.22261420.20541320146299

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