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- PDB-8sjw: [4T28] Self-assembling right-handed tensegrity triangle with 28 i... -

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Basic information

Entry
Database: PDB / ID: 8sjw
Title[4T28] Self-assembling right-handed tensegrity triangle with 28 interjunction base pairs and R3 symmetry
Components
  • DNA (28-MER)
  • DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')
  • DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')
  • DNA (5'-D(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.64 Å
AuthorsJanowski, J. / Vecchioni, S. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 6items
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
Human Frontier Science Program (HFSP)RPG0010/2017 France
National Science Foundation (NSF, United States)DMR-1420073 United States
National Aeronautics and Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Engineering tertiary chirality in helical biopolymers.
Authors: Janowski, J. / Pham, V.A.B. / Vecchioni, S. / Woloszyn, K. / Lu, B. / Zou, Y. / Erkalo, B. / Perren, L. / Rueb, J. / Madnick, J. / Mao, C. / Saito, M. / Ohayon, Y.P. / Jonoska, N. / Sha, R.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')
B: DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')
C: DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')
D: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)25,7724
Polymers25,7724
Non-polymers00
Water00
1
A: DNA (5'-D(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')
B: DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')
C: DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')
D: DNA (28-MER)

A: DNA (5'-D(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')
B: DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')
C: DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')
D: DNA (28-MER)

A: DNA (5'-D(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')
B: DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')
C: DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')
D: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)77,31512
Polymers77,31512
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)227.624, 227.624, 91.414
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(P*CP*AP*TP*CP*TP*AP*GP*CP*TP*CP*GP*TP*GP*GP*AP*CP*TP*GP*AP*T)-3')


Mass: 6124.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*AP*TP*CP*AP*GP*TP*GP*GP*CP*AP*GP*T)-3')


Mass: 4295.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*AP*CP*TP*GP*CP*CP*TP*GP*AP*AP*TP*TP*AP*CP*TP*GP*AP*CP*CP*G)-3')


Mass: 6736.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (28-MER)


Mass: 8614.567 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: 17.68 Å3/Da / Density % sol: 93.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338K-293K at 0.4K/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: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 7.318→82.931 Å / Num. obs: 1653 / % possible obs: 81.2 % / Redundancy: 10.9 % / Biso Wilson estimate: 254.27 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
7.318-8.34611.10.92090.3651
16.578-82.9311120.12060.999199.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W6W

5w6w


Resolution: 7.64→41.47 Å / SU ML: 0.5218 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.7357
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1924 109 6.84 %
Rwork0.177 1484 -
obs0.1787 1593 74.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 574.24 Å2
Refinement stepCycle: LAST / Resolution: 7.64→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1716 0 0 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881922
X-RAY DIFFRACTIONf_angle_d0.89312958
X-RAY DIFFRACTIONf_chiral_restr0.0452334
X-RAY DIFFRACTIONf_plane_restr0.004684
X-RAY DIFFRACTIONf_dihedral_angle_d38.8372826
LS refinement shellResolution: 7.64→41.47 Å
RfactorNum. reflection% reflection
Rfree0.1924 109 -
Rwork0.177 1484 -
obs--74.72 %

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