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- PDB-8cyn: [2T7+20bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Tria... -

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Basic information

Entry
Database: PDB / ID: 8cyn
Title[2T7+20bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle with 20 bp Sticky-End Linker
Components
  • DNA (5'-D(*GP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')
  • DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / tensegrity triangle / synthetic construct / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.45 Å
AuthorsLu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CTS1120890 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CHE-1708776 United States
Office of Naval Research (ONR)N000141110729 United States
Office of Naval Research (ONR)N000140911118 United States
Department of Energy (DOE, United States)DESC0007991 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles.
Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.pdb_format_compatible
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
X: DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')
Y: DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)25,0666
Polymers25,0666
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
X: DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')
Y: DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')

A: DNA (5'-D(*GP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
X: DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')
Y: DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')

A: DNA (5'-D(*GP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
X: DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')
Y: DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)75,19918
Polymers75,19918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_565-x,-y+1,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/21
crystal symmetry operation6_665x-y+1,x+1,z+1/21
Unit cell
Length a, b, c (Å)231.034, 231.034, 100.851
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

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DNA chain , 6 types, 6 molecules ABCDXY

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


Mass: 6433.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')


Mass: 2082.400 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: DNA chain DNA (5'-D(P*GP*AP*TP*GP*CP*TP*GP*AP*CP*GP*TP*AP*GP*TP*AP*GP*CP*AP*GP*A)-3')


Mass: 6223.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*CP*TP*CP*TP*GP*CP*TP*AP*CP*TP*AP*CP*GP*TP*CP*AP*GP*CP*A)-3')


Mass: 6069.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 31 Å3/Da / Density % sol: 96.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA
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: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 9.45→90.06 Å / Num. obs: 1358 / % possible obs: 86.1 % / Redundancy: 18 % / Biso Wilson estimate: 505.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.8
Reflection shellResolution: 9.45→10.85 Å / Num. unique obs: 194 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R96

7r96


Resolution: 9.45→50.02 Å / SU ML: 0.3214 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.144 69 5.31 %
Rwork0.0957 1231 -
obs0.0975 1300 63.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 977.02 Å2
Refinement stepCycle: LAST / Resolution: 9.45→50.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1675 0 0 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511874
X-RAY DIFFRACTIONf_angle_d0.76242879
X-RAY DIFFRACTIONf_chiral_restr0.0398326
X-RAY DIFFRACTIONf_plane_restr0.003582
X-RAY DIFFRACTIONf_dihedral_angle_d35.6766800
LS refinement shellResolution: 9.45→50.02 Å
RfactorNum. reflection% reflection
Rfree0.144 69 -
Rwork0.0957 1231 -
obs--63.17 %

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