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- PDB-9ckh: [d2d3-2Ag] Tensegrity triangle with deazapurines on the helical a... -

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Basic information

Entry
Database: PDB / ID: 9ckh
Title[d2d3-2Ag] Tensegrity triangle with deazapurines on the helical and center strands with two deazaA:Ag+:T base pairs
Components
  • DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / Tensegrity triangle / deaza / Ag+ / mmDNA
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.92 Å
AuthorsVecchioni, S. / Jong, M.A. / Woloszyn, K. / Sha, R. / Ohayon, Y.P. / Gallindo, M.A. / Lopez Chamorro, C.
Funding support United States, 4items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
National Science Foundation (NSF, United States)CCF-2106790 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
CitationJournal: To Be Published
Title: Deazapurine metal-mediated nanostructures
Authors: Lopez Chamorro, C. / Jong, M.A.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 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*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0006
Polymers12,7854
Non-polymers2162
Water00
1
A: DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00118
Polymers38,35412
Non-polymers6476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)123.277, 123.277, 62.265
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: DNA chain DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')


Mass: 6447.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')


Mass: 2079.436 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*C)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 at 0.4 degree /hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979346 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979346 Å / Relative weight: 1
ReflectionResolution: 5.92→19.67 Å / Num. obs: 2128 / % possible obs: 86.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 244.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
5.922-6.7371.11920.5631
11.101-19.6727.61920.9991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 5.92→19.67 Å / SU ML: 0.8329 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.8478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1793 114 5.36 %
Rwork0.1605 2014 -
obs0.1621 2128 78.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 260.18 Å2
Refinement stepCycle: LAST / Resolution: 5.92→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084956
X-RAY DIFFRACTIONf_angle_d1.45271467
X-RAY DIFFRACTIONf_chiral_restr0.0656153
X-RAY DIFFRACTIONf_plane_restr0.005842
X-RAY DIFFRACTIONf_dihedral_angle_d38.7412354
LS refinement shellResolution: 5.92→19.67 Å
RfactorNum. reflection% reflection
Rfree0.1793 114 -
Rwork0.1605 2014 -
obs--78.99 %

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