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- PDB-8dag: [8 bp center] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle -

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Basic information

Entry
Database: PDB / ID: 8dag
Title[8 bp center] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*GP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*C)-3')
KeywordsDNA / tensegrity triangle / synthetic construct / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.16 Å
AuthorsLu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CTS1120890 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CHE-1708776 United States
Office of Naval Research (ONR)N000141110729 United States
Office of Naval Research (ONR)N000140911118 United States
Department of Energy (DOE, United States)DESC0007991 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles.
Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R.
History
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 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*TP*GP*TP*GP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-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*TP*GP*TP*GP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

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

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*GP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-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_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)130.428, 130.428, 53.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*GP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6497.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*CP*AP*CP*A)-3')


Mass: 2371.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*TP*GP*C)-3')


Mass: 1496.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 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: 10.25 Å3/Da / Density % sol: 88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA
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: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 6.16→65.21 Å / Num. obs: 1054 / % possible obs: 89.3 % / Redundancy: 19.8 % / Biso Wilson estimate: 500.14 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.7
Reflection shellResolution: 6.16→7.02 Å / Num. unique obs: 211 / CC1/2: 0.344

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R96

7r96


Resolution: 6.16→42.69 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1267 54 5.19 %
Rwork0.1203 987 -
obs0.1213 1041 81.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 684.79 Å2
Refinement stepCycle: LAST / Resolution: 6.16→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156956
X-RAY DIFFRACTIONf_angle_d1.59931467
X-RAY DIFFRACTIONf_chiral_restr0.0903166
X-RAY DIFFRACTIONf_plane_restr0.010842
X-RAY DIFFRACTIONf_dihedral_angle_d38.2878406
LS refinement shellResolution: 6.16→42.69 Å
RfactorNum. reflection% reflection
Rfree0.1267 54 -
Rwork0.1203 987 -
obs--81.52 %
Refinement TLS params.Method: refined / Origin x: 50.3302978637 Å / Origin y: -29.7575317618 Å / Origin z: 10.4001421056 Å
111213212223313233
T8.6872802171 Å2-0.296798462369 Å20.757368863671 Å2-7.49142525327 Å2-0.121242970205 Å2--8.73804455758 Å2
L21.5733759082 °215.5411169652 °27.52099630222 °2--1.59255268994 °213.590478372 °2---15.3817355915 °2
S0.606007005972 Å °-0.441594770165 Å °-0.608024729508 Å °1.4093815626 Å °-0.435960354791 Å °-1.35153601327 Å °-2.10753250496 Å °-1.59926019166 Å °-0.175534989797 Å °
Refinement TLS groupSelection details: all

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