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- PDB-8sl5: [2T13] Self-assembling left-handed two-turn tensegrity triangle w... -

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Basic information

Entry
Database: PDB / ID: 8sl5
Title[2T13] Self-assembling left-handed two-turn tensegrity triangle with 13 interjunction base pairs and R3 symmetry
Components
  • DNA (5'-D(*GP*AP*GP*CP*CP*TP*GP*AP*CP*TP*AP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*TP*GP*GP*C)-3')
  • DNA (5'-D(P*CP*GP*TP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*TP*AP*GP*TP*CP*AP*CP*CP*AP*CP*G)-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: 6.55 Å
AuthorsVecchioni, S. / Janowski, J. / 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 21, 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(*GP*AP*GP*CP*CP*TP*GP*AP*CP*TP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*TP*GP*GP*AP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(P*TP*GP*TP*AP*GP*TP*CP*AP*CP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*CP*TP*GP*AP*CP*TP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*TP*GP*GP*AP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*TP*GP*GP*C)-3')
D: DNA (5'-D(P*TP*GP*TP*AP*GP*TP*CP*AP*CP*CP*AP*CP*G)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
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)111.886, 111.886, 69.191
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
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*CP*TP*GP*AP*CP*TP*AP*CP*A)-3')


Mass: 3960.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*TP*GP*GP*AP*CP*A)-3')


Mass: 2451.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*TP*GP*GP*C)-3')


Mass: 2433.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*GP*TP*AP*GP*TP*CP*AP*CP*CP*AP*CP*G)-3')


Mass: 3951.586 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: 6.51 Å3/Da / Density % sol: 81.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / 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: 0.99187 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 6.548→55.943 Å / Num. obs: 496 / % possible obs: 81.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 439.41 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
6.548-8.8511.42480.8441
8.897-55.9438.82480.9891

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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 8SJN

8sjn


Resolution: 6.55→32.3 Å / SU ML: 0.8174 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3488 16 3.31 %
Rwork0.203 467 -
obs0.2055 483 77.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 579.51 Å2
Refinement stepCycle: LAST / Resolution: 6.55→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046956
X-RAY DIFFRACTIONf_angle_d0.68711467
X-RAY DIFFRACTIONf_chiral_restr0.0346166
X-RAY DIFFRACTIONf_plane_restr0.002442
X-RAY DIFFRACTIONf_dihedral_angle_d38.2396406
LS refinement shellResolution: 6.55→32.3 Å
RfactorNum. reflection% reflection
Rfree0.3488 16 -
Rwork0.203 467 -
obs--77.4 %
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)
18.718221400945.997622130286.442939887426.022337157585.933297262436.1612929069-6.09007067833-0.06194998365111.631531820360.609847800413.461025118045.785862484363.81386497227-0.6546114688910.7438214557124.96402936407-1.651080539930.8716970589398.992555029650.2198362928614.1597451193519.1593097605-14.487099263210.8545942063
22.837867788873.99521291996-0.3237435900245.67312158436-0.3670472991291.21112946536-0.1556471185671.561523934880.7492373563280.6922540608270.4729443973351.587772621230.0410170855962-0.730332237734-1.926688043766.763006987433.81224334704-0.8293489092138.80001132936-3.532989671576.826710624743.49180975252-27.46259524040.17782166307
33.963244084242.617020312150.627836695763.93136074987-0.08173421014430.9107911898140.8192394027790.289714247799-0.3155420812480.661365377852-0.8291735593471.27010700429-0.596831721143-0.304106579911.083931670233.67650652413-1.996540106262.411277302626.449994317350.83236223778.4620435151217.8073003041-29.84235818633.04654213845
44.66956051733-6.5037104145-4.642728483529.107741026566.466879922734.44539579896-0.191481560373-2.938438468680.2918844660362.234670644894.50536264605-2.21568414063-2.08116411667-0.655445311924-0.4978926348586.952382018851.16777335444-0.4427453352977.404100318080.1427250340781.8930499062612.8292859362-12.15360612575.54464433473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 18)AA6 - 18
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 8)BB1 - 8
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 13)CC6 - 13
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 13)DD1 - 13

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