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- PDB-7u3x: [F233] Self-assembling tensegrity triangle with two turns, three ... -

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Basic information

Entry
Database: PDB / ID: 7u3x
Title[F233] Self-assembling tensegrity triangle with two turns, three turns and three turns of DNA per axis by extension with P1 symmetry
Components
  • (DNA (31-MER)) x 2
  • DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
  • DNA (5'-D(*TP*CP*TP*AP*GP*CP*AP*TP*AP*GP*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*TP*AP*GP*CP*GP*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*A)-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: 5.68 Å
AuthorsWoloszyn, K. / Vecchioni, S. / 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
A: DNA (31-MER)
E: DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')
D: DNA (5'-D(*TP*GP*CP*GP*CP*TP*AP*GP*CP*GP*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
B: DNA (31-MER)
F: DNA (5'-D(*TP*CP*TP*AP*GP*CP*AP*TP*AP*GP*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
C: DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
M: DNA (5'-D(P*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)50,9767
Polymers50,9767
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-6 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.961, 100.275, 102.065
Angle α, β, γ (deg.)100.577, 100.806, 102.394
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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DNA chain , 7 types, 7 molecules AEDBFCM

#1: DNA chain DNA (31-MER)


Mass: 9532.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')


Mass: 4302.788 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*AP*GP*CP*GP*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 7408.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (31-MER)


Mass: 9537.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*TP*CP*TP*AP*GP*CP*AP*TP*AP*GP*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')


Mass: 7464.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')


Mass: 6417.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(P*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*A)-3')


Mass: 6313.090 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: MOPS, Magnesium sulfate, Sodium hydroxide / Temp details: 338-293 at 0.4/hr, 293-277 at 0.1/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 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 5.68→97.489 Å / Num. obs: 5122 / % possible obs: 87.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 400.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
5.68-6.143.72570.481
17.156-97.4893.72550.9981

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Processing

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

3gbi


Resolution: 5.68→41.05 Å / SU ML: 0.6757 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.6849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.179 273 5.37 %
Rwork0.1238 4807 -
obs0.1262 5080 68.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 441.05 Å2
Refinement stepCycle: LAST / Resolution: 5.68→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3385 0 0 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03333793
X-RAY DIFFRACTIONf_angle_d2.60335841
X-RAY DIFFRACTIONf_chiral_restr0.1677658
X-RAY DIFFRACTIONf_plane_restr0.0141166
X-RAY DIFFRACTIONf_dihedral_angle_d42.85121633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.68-7.150.3481930.3231399X-RAY DIFFRACTION40.52
7.15-41.050.16411800.11223408X-RAY DIFFRACTION96.92
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)
14.52620662336-2.9133682652-2.696788371328.66408871532-0.7466277269220.704904414441-0.9323650081850.42160891060.545736930173-0.9582569105511.17095082816-6.05519871271-4.540867991061.78058263483-0.7351210547988.006274940730.135873184897-0.9377923056762.49063143432-1.351743593033.3047084947514.713007258421.3143560107-3.13736617764
20.866367728004-1.2453079904-1.580955697973.761910855312.421454881352.800178734780.7174927419151.76966145427-1.286114117141.12588420117-0.442240893808-1.20029311740.4446526965850.3942541936570.3224248599013.24285329127-0.135635915211-3.262164846254.8171645696-4.487956196626.1971483983424.7239827203-8.398573362197.11104845482
30.256643732923-1.01973783354-0.1355810157453.61387334975-0.4915234661920.1923897098310.605071573712-1.962250849792.365258569841.828834598260.1625981621070.528742574723-2.92606984311-0.5933736849340.8824875915347.80173275561-0.851923808930.862000065061.43668573861-1.801970957144.829962462616.5376514314939.5846825375-6.45092080778
45.14930486203-0.587272195461-2.646496089663.867612108-0.9697577339041.782159949580.110050649696-1.51079670963-1.15660588127-0.167359058241-3.174096712832.0692562837-0.120872546712-0.9950944998521.032995900756.95269664735-2.58313605035-0.2682071499983.84326840369-1.895403471431.5837576942-10.949296769412.473170514217.9294750019
51.92484722241-0.0703218187487-1.221050186180.2521294474410.5464003156691.08214531522-0.634908614393-2.64775118656-1.384187137923.787428083250.688709841892-2.13297078987-0.2457718432321.444590468870.0174955321387.250858290490.625066745791-1.420569799217.143771820590.07310710179070.844553049765-16.25188069862.9917594609936.8437621262
68.78533883645-1.269660127973.433860310176.7800575982-6.141410920055.945035316911.06654448011-1.7738193766-0.7367058799592.88745502612.11010667395-0.459864281699-3.953187837981.29946368036-0.3676515521612.141866972-0.371328181479-0.6040643516665.04022220953-2.422901030512.193787853721.6591220241-6.3838250338215.2982159567
71.993004509035.733862364582.030744480876.48975552177-1.30362289351.97652582097-0.538258221967-0.743034054015-2.12923013326-1.254233935691.73688830848-3.92503060038-1.68071683235-2.37206734360.4454548595694.522392186972.288030532041.325777493834.36129276368-0.5205269949632.858504312993.289498863685.183148135814.99792230282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 131)AA101 - 131
2X-RAY DIFFRACTION2(chain 'E' and resid 101 through 114)EB101 - 114
3X-RAY DIFFRACTION3(chain 'D' and resid 101 through 124)DC101 - 124
4X-RAY DIFFRACTION4(chain 'B' and resid 101 through 131)BD101 - 131
5X-RAY DIFFRACTION5(chain 'F' and resid 101 through 124)FE101 - 124
6X-RAY DIFFRACTION6(chain 'C' and resid 101 through 121)CF101 - 121
7X-RAY DIFFRACTION7(chain 'M' and resid 101 through 121)MG101 - 121

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