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- PDB-9d6v: [F:Au+/Ag+:F-pH8] Heterobimetallic base pair with Ag+ and Au+ bet... -

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Basic information

Entry
Database: PDB / ID: 9d6v
Title[F:Au+/Ag+:F-pH8] Heterobimetallic base pair with Ag+ and Au+ between a 2-thio-dT homopair, crystallized in the presence of Ag+, Au+ and Cu+
Components
  • (DNA) x 2
  • DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA / Tensegrity triangle / gold / silver / heterobimetallic
Function / homologySILVER ION / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.87 Å
AuthorsVecchioni, S. / Imstepf, L. / Lu, B. / Woloszyn, K. / Sha, R. / Ohayon, Y.P.
Funding support China, United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)GCR-2317843 China
Department of Energy (DOE, United States)DE-SC0007991 United States
Office of Naval Research (ONR)N000141912596 United States
CitationJournal: To Be Published
Title: Thiothymidine metal base pairs
Authors: Vecchioni, S. / Imstepf, L. / Lu, B. / Woloszyn, K. / Sha, R. / Ohayon, Y.P.
History
DepositionAug 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: 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
B: DNA
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1246
Polymers12,8204
Non-polymers3052
Water00
1
A: DNA
B: DNA
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)39,37318
Polymers38,45912
Non-polymers9156
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)105.937, 105.937, 92.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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DNA chain , 4 types, 4 molecules ABCD

#1: DNA chain DNA


Mass: 6479.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA


Mass: 2082.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION

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Details

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: 7.13 Å3/Da / Density % sol: 82.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 at 0.4/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92012 Å / Relative weight: 1
ReflectionResolution: 4.866→65.226 Å / Num. obs: 2386 / % possible obs: 85.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 209.04 Å2 / CC1/2: 0.979 / Net I/σ(I): 4.6
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
4.866-5.6551.62000.4041
10.194-65.2268.92010.9781

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.87→52.97 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 38.1849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 100 4.19 %
Rwork0.2384 2286 -
obs0.2405 2386 65.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 247.97 Å2
Refinement stepCycle: LAST / Resolution: 4.87→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 572 288 0 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072958
X-RAY DIFFRACTIONf_angle_d0.99341471
X-RAY DIFFRACTIONf_chiral_restr0.0515159
X-RAY DIFFRACTIONf_plane_restr0.004542
X-RAY DIFFRACTIONf_dihedral_angle_d36.774435
LS refinement shellResolution: 4.87→52.97 Å
RfactorNum. reflection% reflection
Rfree0.2688 100 -
Rwork0.2384 2286 -
obs--65.73 %

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