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- PDB-8sjq: [3T16] Self-assembling right-handed tensegrity triangle with 16 i... -

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Basic information

Entry
Database: PDB / ID: 8sjq
Title[3T16] Self-assembling right-handed tensegrity triangle with 16 interjunction base pairs and R3 symmetry
Components
  • DNA (5'-D(*CP*AP*GP*CP*AP*TP*GP*CP*CP*TP*GP*AP*TP*AP*CP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*AP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')
  • DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*CP*AP*CP*CP*AP*CP*GP*A)-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: 6.19 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 Aeronautic 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(*CP*AP*GP*CP*AP*TP*GP*CP*CP*TP*GP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)18,9784
Polymers18,9784
Non-polymers00
Water0
1
A: DNA (5'-D(*CP*AP*GP*CP*AP*TP*GP*CP*CP*TP*GP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)56,93512
Polymers56,93512
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)167.658, 167.658, 91.904
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(*CP*AP*GP*CP*AP*TP*GP*CP*CP*TP*GP*AP*TP*AP*CP*CP*GP*CP*A)-3')


Mass: 5774.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')


Mass: 4883.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*AP*TP*GP*C)-3')


Mass: 4616.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')


Mass: 3703.416 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: 13.1 Å3/Da / Density % sol: 90.61 %
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: 6.16→83.829 Å / Num. obs: 1444 / % possible obs: 80.9 % / Redundancy: 11 % / Biso Wilson estimate: 328.85 Å2 / CC1/2: 1 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
6.16-7.19711.30.92080.4911
13.663-83.82911.324.62051199.5

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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: 6.19→35.23 Å / SU ML: 0.3589 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.5048
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1374 95 6.77 %
Rwork0.1087 1308 -
obs0.1107 1403 64.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 571.2 Å2
Refinement stepCycle: LAST / Resolution: 6.19→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1265 0 0 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051416
X-RAY DIFFRACTIONf_angle_d0.69572177
X-RAY DIFFRACTIONf_chiral_restr0.0356246
X-RAY DIFFRACTIONf_plane_restr0.00462
X-RAY DIFFRACTIONf_dihedral_angle_d37.0008606
LS refinement shellResolution: 6.19→35.23 Å
RfactorNum. reflection% reflection
Rfree0.1374 95 -
Rwork0.1087 1308 -
obs--64.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.061056964147.462974200472.746843841882.65719748743-10.68118468568.693936379732.64584867819-4.08146164153-11.51504290252.36092829464-2.24595354431-6.392839417530.228697597682-0.152712285045-3.748239045165.24316820519-1.33215280055-1.044935148256.57316874139-3.42087064836.937054201430.7838352773-6.1729662977-7.04612799873
22.268970695611.58560755505-0.2163946267042.2659009426211.0536296259.0022549775510.9832728145-2.16310738950.6668191864688.26653417931-2.2566311453-5.66382139651.33295711701-4.536148977935.017145450553.572632415431.009818795131.790341798346.48143319049-1.596702341795.8763572721219.3695325929-3.2510783797-13.746340174
33.02990680645-4.24634194608-0.3107659016413.465852673232.152202825934.672497515711.06227013188-0.675017855642-0.120603400357-0.585525525874-2.137789162822.14001369288-2.965512937296.013166045760.3804483177145.09939578329-0.720128719976-0.910013777097.97973418336-1.545426630795.2647918011140.9832739782-0.867363903941-15.0990070579
45.163182407350.830327046377-2.224737258767.88686202729-4.703212642033.402335355142.745562653778.63234086017-1.56533372190.0672798649754-2.472192184087.86024438957-4.263351407670.8385028378372.99409370575.393989172180.3948902256380.7499015057577.86435138364-3.750807964074.9195330686530.03436193123.48732060496-22.0968985327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 119)AA101 - 119
2X-RAY DIFFRACTION2(chain 'B' and resid 101 through 116)BB101 - 116
3X-RAY DIFFRACTION3(chain 'C' and resid 101 through 115)CC101 - 115
4X-RAY DIFFRACTION4(chain 'D' and resid 101 through 112)DD101 - 112

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