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- PDB-7u3z: [F244] Self-assembling tensegrity triangle with two turns, four t... -

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Basic information

Entry
Database: PDB / ID: 7u3z
Title[F244] Self-assembling tensegrity triangle with two turns, four turns and four turns of DNA per axis by extension with P1 symmetry
Components
  • (DNA (35-MER)) x 2
  • (DNA (42-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*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: 7.55 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 1.2Aug 16, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.pdb_format_compatible
Revision 1.3Oct 25, 2023Group: Refinement description / Category: 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 (42-MER)
E: DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')
D: DNA (35-MER)
B: DNA (42-MER)
F: DNA (35-MER)
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)64,5717
Polymers64,5717
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.638, 135.539, 136.111
Angle α, β, γ (deg.)100.055, 103.071, 96.364
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 (42-MER)


Mass: 12950.317 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 (35-MER)


Mass: 10786.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (42-MER)


Mass: 12916.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (35-MER)


Mass: 10883.991 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: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 7.55→65.904 Å / Num. obs: 3421 / % possible obs: 81.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 273.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
7.55-8.6163.62010.4291
22.145-65.9043.32010.9991

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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: 7.55→63.63 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.6435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 146 4.33 %
Rwork0.168 3229 -
obs0.1704 3375 59.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 963.58 Å2
Refinement stepCycle: LAST / Resolution: 7.55→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4299 0 0 4299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774816
X-RAY DIFFRACTIONf_angle_d0.97937415
X-RAY DIFFRACTIONf_chiral_restr0.0529838
X-RAY DIFFRACTIONf_plane_restr0.0052210
X-RAY DIFFRACTIONf_dihedral_angle_d41.29422074
LS refinement shellResolution: 7.55→63.63 Å
RfactorNum. reflection% reflection
Rfree0.2194 146 -
Rwork0.168 3229 -
obs--59.09 %
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)
11.45582903221-3.82636218722-2.261531029135.764275711633.053289281341.18420905702-0.706971767182-2.15963654154-1.816774166245.10494339716-2.547929360882.72017162316-9.40204874338-1.523937363921.1778962226710.2561446182-0.320196793959-0.8749141697135.27982066786-1.172196243937.3810226481616.5463.053-5.572
22.94310600921-3.710045065910.7028525892869.22337228821.539387686271.41431308187-0.33352870054-1.30842940679-2.670680584484.74026642725-0.05728507858242.110817373922.41547862801-1.37639194982-0.3622682023035.31449187351-2.29995069588-0.7219984510165.85944205043-0.1557484557885.3664563861324.018-9.6055.187
31.755058270732.398603380841.590528319453.501356922622.02713082972.880400340090.580735390913-4.222176792073.564478673521.774981056752.83396839848-1.238241337531.456928340294.42617187991.0054055402214.1699552605-3.413126388116.264523013679.45425843061-3.9035813951410.154625714411.08956.092-6.602
41.24362710099-1.896546131150.8785498205686.209575017730.7982270456290.5610945893621.21873116959-3.21933419827-3.01846468535-2.874073277072.639108271692.038427158690.6697377442490.2453452701014.289823918488.632525270061.799455213721.6190125013914.95086043922.064638158282.71349914525-14.82911.10134.759
50.722065555981-1.79221734816-0.08791888952944.48878868075-0.107333328101-0.0444448459606-2.954444093-1.620432026763.85785203832-0.224731770119-2.610787559793.37699679692-0.3097211939610.218642450388-1.602891335186.839155517552.394935326830.86532201502214.0134051346-1.992083065538.16644702313-29.7785.44884.123
64.154167258210.2664018516371.59580307182-0.3597198112-0.5084112354060.161509024081-0.463221260439-0.228175482527-2.50486409024-4.489066216742.958359857560.4619175218793.01395153629-6.273509606430.45400636072612.2949945349-0.348518437165-1.420079305856.663201782882.13211113394.694135116980.881-6.78915.404
73.349481368822.815968911881.467896691272.718430365050.5178477958991.981509424942.465311918480.6741331568755.387666480953.25317388106-0.4376140451622.91495282972-3.448971487410.713268575927-3.122598949917.34054657594-0.8173868757270.4534656820989.797243776251.264476591914.444753591364.5724.3295.069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 101:142 )A101 - 142
2X-RAY DIFFRACTION2( CHAIN E AND RESID 101:114 )E101 - 114
3X-RAY DIFFRACTION3( CHAIN D AND RESID 101:135 )D101 - 135
4X-RAY DIFFRACTION4( CHAIN B AND RESID 101:142 )B101 - 142
5X-RAY DIFFRACTION5( CHAIN F AND RESID 101:114 )F101 - 114
6X-RAY DIFFRACTION6( CHAIN C AND RESID 101:121 )C101 - 121
7X-RAY DIFFRACTION7( CHAIN M AND RESID 101:121 )M101 - 121

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