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- PDB-9c6h: [d3] Tensegrity triangle with deazapurine center strand (strand 3... -

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Basic information

Entry
Database: PDB / ID: 9c6h
Title[d3] Tensegrity triangle with deazapurine center strand (strand 3) in R3
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*(7DA)P*CP*(7DA)P*CP*CP*(7GU)P*T)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
KeywordsDNA / self-assembling / tensegrity triangle / deaza
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.18 Å
AuthorsVecchioni, S. / Sha, R. / Ohayon, Y. / Galindo, M. / Lopez-Chamorro, C. / Jong, M.
Funding support United States, 5items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
National Science Foundation (NSF, United States)CCF-2106790 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
CitationJournal: To Be Published
Title: Deazapurine DNA Nanostructures
Authors: Vecchioni, S.
History
DepositionJun 7, 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*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*(7DA)P*CP*(7DA)P*CP*CP*(7GU)P*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7944
Polymers12,7944
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*(7DA)P*CP*(7DA)P*CP*CP*(7GU)P*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,38312
Polymers38,38312
Non-polymers00
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)107.520, 107.520, 88.789
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*A)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*(7DA)P*CP*(7DA)P*CP*CP*(7GU)P*T)-3')


Mass: 2079.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 2724.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 at 0.4 degrees/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: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 4.176→32.718 Å / Num. obs: 1952 / % possible obs: 85.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 297.1 Å2 / CC1/2: 1 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
4.176-4.6325.21950.2761
10.018-32.7185.219511

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.18→32.13 Å / SU ML: 0.4966 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 40.7154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 115 6.1 %
Rwork0.2156 1769 -
obs0.2177 1884 66.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 305.23 Å2
Refinement stepCycle: LAST / Resolution: 4.18→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078956
X-RAY DIFFRACTIONf_angle_d1.13691467
X-RAY DIFFRACTIONf_chiral_restr0.0588163
X-RAY DIFFRACTIONf_plane_restr0.006642
X-RAY DIFFRACTIONf_dihedral_angle_d40.9295394
LS refinement shellResolution: 4.18→32.13 Å
RfactorNum. reflection% reflection
Rfree0.253 115 -
Rwork0.2156 1769 -
obs--66.24 %
Refinement TLS params.Method: refined / Origin x: 20.5170348701 Å / Origin y: 0.605394962128 Å / Origin z: 11.9067633925 Å
111213212223313233
T2.02697782552 Å2-0.0231026341576 Å2-0.392596799755 Å2-2.83464698048 Å2-0.416387822896 Å2--2.57300162122 Å2
L8.79074512609 °2-2.39810618863 °2-13.0503108954 °2-12.9223123184 °24.69385467566 °2--8.63479269664 °2
S1.82786898839 Å °-0.04991088186 Å °1.11204613206 Å °0.0747011429566 Å °-0.317964068374 Å °-1.76788621651 Å °-1.62420913199 Å °-0.402784110707 Å °-1.17149365869 Å °
Refinement TLS groupSelection details: all

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