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- PDB-8d93: [2T7] Self-assembling tensegrity triangle with R3 symmetry at 2.9... -

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Basic information

Entry
Database: PDB / ID: 8d93
Title[2T7] Self-assembling tensegrity triangle with R3 symmetry at 2.96 A resolution, update and junction cut for entry 3GBI
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials / linking number
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsVecchioni, S. / Woloszyn, K. / Lu, B. / Sha, R. / Ohayon, Y.P. / Seeman, N.C.
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
Citation
Journal: Small / Year: 2023
Title: The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles.
Authors: Vecchioni, S. / Lu, B. / Janowski, J. / Woloszyn, K. / Jonoska, N. / Seeman, N.C. / Mao, C. / Ohayon, Y.P. / Sha, R.
#1: Journal: To Be Published
Title: Mirror Nanomaterials: Self-Assembly of Left-Handed, Anti-Tensegrity DNA Triangles
Authors: Vecchioni, S. / Janowski, J. / Lu, B. / Ohayon, Y.P. / Sha, R. / Woloszyn, K. / Mao, C. / Seeman, N.C.
History
DepositionJun 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
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 (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

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

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-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)105.547, 105.547, 96.268
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*AP*GP*CP*CP*TP*GP*TP*A)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 2724.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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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: 7.53 Å3/Da / Density % sol: 83.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 40 mM Tris, 2 mM EDTA, 20 mM acetic acid, 125 mM magnesium acetate, 583 mM ammonium sulfate
Temp details: 338-293 degrees C at 0.4 degrees C / hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.007 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.96→66.29 Å / Num. obs: 3342 / % possible obs: 57 % / Redundancy: 10.4 % / Biso Wilson estimate: 44.76 Å2 / CC1/2: 1 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
2.96-3.4110.331990.921
10.42-66.2910.836.81960.9991

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Processing

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

3gbi


Resolution: 2.96→41.29 Å / SU ML: 0.041 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 176 5.28 %
Rwork0.1847 3157 -
obs0.1869 3333 39.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.01 Å2
Refinement stepCycle: LAST / Resolution: 2.96→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 794 61 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115955
X-RAY DIFFRACTIONf_angle_d1.41021463
X-RAY DIFFRACTIONf_chiral_restr0.0715166
X-RAY DIFFRACTIONf_plane_restr0.010342
X-RAY DIFFRACTIONf_dihedral_angle_d42.7284403
LS refinement shellResolution: 2.96→41.29 Å
RfactorNum. reflection% reflection
Rfree0.2258 176 -
Rwork0.1847 3157 -
obs--39.96 %
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)
14.449440261751.253707156211.234560802252.39879897991-0.1536059507890.4544819896810.866044756489-1.47203271808-0.2452958982760.769448342162-0.324284223267-1.409741020690.07569756710270.457485529782-0.8352061339291.60555908015-0.434482029023-0.3334433292711.9412819104-0.5138766885611.3640751985221.317-5.367-1.616
25.91444105936-0.6242876715833.195708817445.37047535724-3.769776882813.948984179291.130925287721.88871667993-0.497315147752-0.9326394180520.572622486624-0.497154614834-0.00708975543066-0.1515622434822.115588696950.521984075396-0.2297520107450.6063386632141.80648016305-0.5980020964341.092236052512.816-6.587-11.052
31.43442708054-0.175867769999-1.810830574720.7218206260962.023806795317.029496517610.1095753676920.14049273230.962409237119-1.03692624756-0.320024604985-0.0191112701454-0.520823378542-1.80085312187-0.2339694732540.923323464417-0.2463437519950.3071186737211.66940344268-0.6401501533281.4026505586712.54310.702-9.944
47.294517998211.205385896812.436272553126.865262745840.4776199818247.15426103091.77658050003-0.311146189458-0.0242015355578-0.407029367899-0.768985904298-1.017414946540.519346598924-0.21048181615-1.647442799540.90610949070.2339258040530.1009574844641.20132164537-0.5742444138161.372011906224.362-0.909-12.561
56.43479108091-1.26490930618-1.262531361162.94519245759-0.851824983610.6954308451770.656565790510.4089996409810.495934129442-1.095743598870.1727068917750.00817806205081-0.829553266584-0.01926050757940.5933587233491.169617692490.2326182147430.1443155633161.27218755186-0.2872013349791.0494074533518.695.349-18.474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 101:112 )A101 - 112
2X-RAY DIFFRACTION2( CHAIN B AND RESID 105:107 )B105 - 107
3X-RAY DIFFRACTION3( CHAIN B AND RESID 111:114 )B111 - 114
4X-RAY DIFFRACTION4( CHAIN C AND RESID 101:114 )C101 - 114
5X-RAY DIFFRACTION5( CHAIN D AND RESID 113:121 )D113 - 121

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