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- PDB-7u3p: [3T7] Self-assembling tensegrity triangle with three turns of DNA... -

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Basic information

Entry
Database: PDB / ID: 7u3p
Title[3T7] Self-assembling tensegrity triangle with three turns of DNA per axis with R3 symmetry
Components
  • DNA (31-MER)
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.06 Å
AuthorsWoloszyn, K. / Vecchioni, S. / Lu, B. / Ma, Y. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 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
Human Frontier Science Program (HFSP)RPG0010/2017 France
National Science Foundation (NSF, United States)DMR-1420073 United States
CitationJournal: Adv Mater / Year: 2022
Title: Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants.
Authors: Woloszyn, K. / Vecchioni, S. / Ohayon, Y.P. / Lu, B. / Ma, Y. / Huang, Q. / Zhu, E. / Chernovolenko, D. / Markus, T. / Jonoska, N. / Mao, C. / Seeman, N.C. / Sha, R.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (31-MER)
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,9764
Polymers18,9764
Non-polymers00
Water00
1
C: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (31-MER)
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')

C: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (31-MER)
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')

C: DNA (5'-D(P*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')
A: DNA (31-MER)
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)56,92912
Polymers56,92912
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)159.208, 159.208, 127.740
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*GP*TP*AP*CP*TP*CP*AP*GP*CP*AP*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 5506.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (31-MER)


Mass: 9562.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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)
#4: 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)

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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: 16.42 Å3/Da / Density % sol: 92.51 % / Description: Rhombohedral
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM MOPS, 125 mM magnesium sulfate
Temp details: 338K to 293K at 0.4K/hr, 293K to 277K at 0.1K/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: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 6.06→93.705 Å / Num. obs: 2042 / % possible obs: 84.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 549.83 Å2 / CC1/2: 0.998 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsRpim(I) allDiffraction-IDCC1/2
6.06-6.81410.92125.5681
14.691-93.70510.920310.998

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASER1.18.2_3874phasing
autoPROCdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBI

3gbi


Resolution: 6.06→37.55 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 118 6.26 %
Rwork0.1277 1767 -
obs0.1303 1885 64.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 638.96 Å2
Refinement stepCycle: LAST / Resolution: 6.06→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1268 0 0 1268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02581418
X-RAY DIFFRACTIONf_angle_d2.33562177
X-RAY DIFFRACTIONf_chiral_restr0.1366247
X-RAY DIFFRACTIONf_plane_restr0.011162
X-RAY DIFFRACTIONf_dihedral_angle_d43.2696604
LS refinement shellResolution: 6.06→37.55 Å
RfactorNum. reflection% reflection
Rfree0.174 118 -
Rwork0.1277 1767 -
obs--64.29 %
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)
16.333715602443.18135630866-1.343632933136.355997049534.034119478654.836067276487.086696562842.959759558131.71570083394-3.37029261181-0.177773601509-0.225847733836-0.254946157065-2.356926902231.694296293048.577523162451.7063322325-2.886296695926.746600839243.258082603268.09203344302-25.114-32.56314.126
24.20954730527-1.88558385538-2.978509373738.992753856652.520878013312.287810915492.270498254381.423694192091.77294259378-2.63088298950.131133838571-2.664305689720.41148803266-0.4230804246931.656842753326.449429713041.10810525963-1.422967188914.667361445523.218474312094.451299129278.228-12.30533.769
38.737245638611.79590310553-7.512801249433.557911446360.2426867019287.63020519506-1.88690186451-0.743544311082-0.7599273494551.36245323664-0.4541978754820.2751496105843.26376679846.217858947651.03474547758.402179560.603468620492-4.439347764857.315647179470.7262797830739.66842289395-29.288-37.04612.78
43.82079482039-0.729425326204-5.528039799393.170905357960.4344831087718.467969046094.74827201729-0.39538716082-1.28913096126-5.67309628915-1.379503417293.263616969792.715755570411.38948094275-3.214411353787.791959858830.268563469022-0.5251448930713.102459376730.9353876533063.876933585975.637-12.99932.431
54.77215430761-1.40115824473-4.923633267450.4100075671791.478653641755.1869715896-0.69217767212-1.52395685818-1.13304556942.424421507962.33999667221-3.524026174263.277001856481.31718991851-1.259706842216.821438342970.245918663269-2.288240394415.96102196010.704950604096.3031213097322.7-5.33845.359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 101:118 )C101 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 101:121 )A101 - 121
3X-RAY DIFFRACTION3( CHAIN A AND RESID 122:131 )A122 - 131
4X-RAY DIFFRACTION4( CHAIN B AND RESID 101:107 )B101 - 107
5X-RAY DIFFRACTION5( CHAIN D AND RESID 109:114 )D109 - 114

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