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- PDB-9uyt: DNA duplex containing gold-mediated 2-thio-cytosine base pairs -

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Basic information

Entry
Database: PDB / ID: 9uyt
TitleDNA duplex containing gold-mediated 2-thio-cytosine base pairs
ComponentsDNA (5'-D(*GP*GP*AP*GP*TP*XP*XP*AP*CP*TP*CP*C)-3')
KeywordsDNA / gold
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsKondo, J. / Kosugi, K. / Sugawara, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Chembiochem / Year: 2025
Title: Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold.
Authors: Kosugi, K. / Sugawara, A. / Iwase, E. / Park, H. / Fujiwara, S. / Kanazawa, H. / Ono, A. / Kondo, J.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: 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*GP*AP*GP*TP*XP*XP*AP*CP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*GP*TP*XP*XP*AP*CP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8254
Polymers7,4312
Non-polymers3942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-18 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.795, 35.795, 61.015
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: DNA chain DNA (5'-D(*GP*GP*AP*GP*TP*XP*XP*AP*CP*TP*CP*C)-3')


Mass: 3715.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MOPs, Spermine,KNO3,MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.03932 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03932 Å / Relative weight: 1
ReflectionResolution: 2.51→31 Å / Num. obs: 5946 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.034 / Net I/σ(I): 31.27
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.51-2.580.3214560.9470.361
2.58-2.650.1874020.980.211
2.65-2.730.1754400.9880.1941
2.73-2.810.1314000.9930.1451
2.81-2.90.13780.9960.1111
2.9-30.0853920.9980.0941
3-3.120.0433580.9990.0481
3.12-3.250.03438810.0371
3.25-3.390.02629810.0291
3.39-3.560.0273450.9990.0311
3.56-3.750.02629410.0291
3.75-3.980.02631310.0291
3.98-4.250.02323010.0251
4.25-4.590.0252680.9990.0281
4.59-5.030.0272480.9990.031
5.03-5.620.0281960.9980.0311
5.62-6.490.0261920.9990.0291
6.49-7.950.0251680.9990.0281
7.95-11.240.0261140.9990.0291
11.24-310.025660.9990.0281

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→31 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 579 9.77 %
Rwork0.1738 --
obs0.1771 5925 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 2 0 490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009544
X-RAY DIFFRACTIONf_angle_d1.064834
X-RAY DIFFRACTIONf_dihedral_angle_d16.567208
X-RAY DIFFRACTIONf_chiral_restr0.03994
X-RAY DIFFRACTIONf_plane_restr0.00524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.770.35681520.33841346X-RAY DIFFRACTION100
2.77-3.170.36721380.27611316X-RAY DIFFRACTION100
3.17-3.980.22841500.18121346X-RAY DIFFRACTION99
4.01-310.13521390.11491338X-RAY DIFFRACTION100

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