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- PDB-9d6u: [F:Au+:F-pH11] Gold base pair with 2-thiothymidine homopair at pH 11.0 -

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Basic information

Entry
Database: PDB / ID: 9d6u
Title[F:Au+:F-pH11] Gold base pair with 2-thiothymidine homopair at pH 11.0
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
  • 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 / mmDNA / gold / pH / thiothymidine
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.21 Å
AuthorsVecchioni, S. / Imstepf, L. / Lu, B. / Woloszyn, K. / Sha, R. / Ohayon, Y.P.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0007991 United States
Office of Naval Research (ONR)N000141912596 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
CitationJournal: To Be Published
Title: Thiopyrimidine 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 (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
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)13,2136
Polymers12,8204
Non-polymers3942
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
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 (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
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 (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
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)39,64018
Polymers38,45912
Non-polymers1,1826
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)106.433, 106.433, 93.032
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

#1: DNA chain DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(DF)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6479.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')


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)
#5: 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: 7.91 Å3/Da / Density % sol: 84.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 11 / Details: 100 mM MOPS, 1.25 M magnesium sulfate

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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: 1.007428 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007428 Å / Relative weight: 1
ReflectionResolution: 4.208→19.344 Å / Num. obs: 3811 / % possible obs: 86.8 % / Redundancy: 5 % / Biso Wilson estimate: 261.46 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
4.208-4.6761920.2531
9.796-19.3441920.991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.21→19.34 Å / SU ML: 0.3329 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.2243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2219 203 5.33 %
Rwork0.1735 3608 -
obs0.1755 3811 67.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 290.08 Å2
Refinement stepCycle: LAST / Resolution: 4.21→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 2 0 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072958
X-RAY DIFFRACTIONf_angle_d1.08871471
X-RAY DIFFRACTIONf_chiral_restr0.0514159
X-RAY DIFFRACTIONf_plane_restr0.005442
X-RAY DIFFRACTIONf_dihedral_angle_d36.9603435
LS refinement shellResolution: 4.21→19.34 Å
RfactorNum. reflection% reflection
Rfree0.2219 203 -
Rwork0.1735 3608 -
obs--67.12 %

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