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- PDB-8sjp: [3T15] Self-assembling DNA motif with 15 base pairs between junct... -

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Basic information

Entry
Database: PDB / ID: 8sjp
Title[3T15] Self-assembling DNA motif with 15 base pairs between junctions and P32 symmetry
Components
  • DNA (5'-D(*CP*AP*GP*CP*TP*GP*AP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')
  • DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.22 Å
AuthorsVecchioni, S. / Janowski, J. / Sha, R. / Ohayon, Y.P.
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
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Engineering tertiary chirality in helical biopolymers.
Authors: Janowski, J. / Pham, V.A.B. / Vecchioni, S. / Woloszyn, K. / Lu, B. / Zou, Y. / Erkalo, B. / Perren, L. / Rueb, J. / Madnick, J. / Mao, C. / Saito, M. / Ohayon, Y.P. / Jonoska, N. / Sha, R.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*AP*GP*CP*TP*GP*AP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')
C: DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')
D: DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,9934
Polymers18,9934
Non-polymers00
Water00
1
A: DNA (5'-D(*CP*AP*GP*CP*TP*GP*AP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')
C: DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')
D: DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')

A: DNA (5'-D(*CP*AP*GP*CP*TP*GP*AP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')
C: DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')
D: DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')

A: DNA (5'-D(*CP*AP*GP*CP*TP*GP*AP*CP*CP*TP*GP*AP*CP*TP*CP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')
C: DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')
D: DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)56,98012
Polymers56,98012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+2/31
crystal symmetry operation3_555-x+y,-x,z+1/31
Unit cell
Length a, b, c (Å)100.632, 100.632, 72.676
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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


Mass: 5445.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*AP*TP*GP*GP*AP*CP*AP*GP*GP*GP*G)-3')


Mass: 4081.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*AP*TP*CP*G)-3')


Mass: 4584.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*GP*CP*TP*CP*CP*TP*GP*TP*GP*GP*TP*CP*AP*GP*C)-3')


Mass: 4881.151 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: 11.19 Å3/Da / Density % sol: 89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338K-293K at 0.4K/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: 5.218→55.815 Å / Num. obs: 1881 / % possible obs: 84.2 % / Redundancy: 9.6 % / Biso Wilson estimate: 318.48 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
5.218-5.98612130.2211
12.999-55.815936.92080.9991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XNA

6xna


Resolution: 5.22→50.32 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.3166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1607 100 5.4 %
Rwork0.093 1753 -
obs0.0959 1853 59.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 314.83 Å2
Refinement stepCycle: LAST / Resolution: 5.22→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1266 0 0 1266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02551416
X-RAY DIFFRACTIONf_angle_d1.98352175
X-RAY DIFFRACTIONf_chiral_restr0.122246
X-RAY DIFFRACTIONf_plane_restr0.011162
X-RAY DIFFRACTIONf_dihedral_angle_d37.7907603
LS refinement shellResolution: 5.22→50.32 Å
RfactorNum. reflection% reflection
Rfree0.1607 100 -
Rwork0.093 1753 -
obs--59.35 %
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)
14.736792244330.1894990350061.659801510937.52562476151-4.225747283533.241874159441.33620637805-2.62348652493-3.29895042292-0.9943647893281.13038211540.3360071763331.314828385343.2835813676-3.473634021.575508448370.493271505538-0.2918671610843.709936659630.06735432826824.242915355633.462-19.859-9.549
27.20278137463.57458334014-4.575387010113.82773148568-0.8447089746073.920285866971.18949237185-1.076758728761.526449392931.39858485694-2.94019912431-3.99140573573-0.3654187210433.622853498070.7271737189821.881240022090.00706079701904-0.1106147503412.895661945640.8786143161113.7900486080535.327-13.3011.682
35.473643874331.52202212337-3.130220537780.414829094396-0.8713622965231.797667454210.413068482362-1.097794556910.716331198832-1.166661456512.06201708337-1.48354575492-0.5446336903841.28957129382.844476932593.678014539350.2099606368741.240966505823.437246709190.2530611568771.665875977396.86-12.8610.371
44.17853666181-0.1508365439810.340256745142.005504361880.9154738026961.97198203341-0.529988552838-0.171189080271-0.8972870671841.043889026622.756453268681.81023082576-1.03261463539-0.00574365587227-2.482564882763.052695779320.155596554099-0.2393662255943.535830485660.3906929901642.4442866942223.682-14.575-17.774
51.382557302371.26707490126-0.5247659561246.808831571614.931788971165.576922561331.98861912227-1.02677645095-2.52512401444-2.01314707904-0.320338579453-3.11841509377-0.441098453789-1.13654962532.23394688991.709277589760.682374971954-0.3273595242272.549229691180.5148319294274.8710368272214.452-8.418-6.503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 1:16 )D1 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:12 )A1 - 12
3X-RAY DIFFRACTION3( CHAIN A AND RESID 13:18 )A13 - 18
4X-RAY DIFFRACTION4( CHAIN B AND RESID 7:19 )B7 - 19
5X-RAY DIFFRACTION5( CHAIN C AND RESID 1:15 )C1 - 15

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