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- PDB-8sz5: [2T5] Self-assembling DNA motif with 5 base pairs between junctio... -

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Basic information

Entry
Database: PDB / ID: 8sz5
Title[2T5] Self-assembling DNA motif with 5 base pairs between junctions and P32 symmetry
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*G)-3')
  • DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*CP*T)-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: 2.89 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)020 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
DepositionMay 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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


Theoretical massNumber of molelcules
Total (without water)12,8466
Polymers12,7974
Non-polymers492
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*G)-3')
B: DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
C: DNA (5'-D(P*CP*AP*CP*GP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*CP*T)-3')
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)38,53818
Polymers38,39212
Non-polymers1466
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)69.089, 69.089, 59.208
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(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*G)-3')


Mass: 3383.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')


Mass: 2997.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*AP*CP*GP*T)-3')


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*CP*T)-3')


Mass: 4936.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 6.38 Å3/Da / Density % sol: 80.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293K 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: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 2.89→59.833 Å / Num. obs: 3687 / % possible obs: 81.5 % / Redundancy: 11 % / Biso Wilson estimate: 55.05 Å2 / CC1/2: 0.997 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
2.892-3.1699.52030.0851
9.45-59.8339.72050.9971

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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 6X8C

6x8c


Resolution: 2.89→34.54 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.5676
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2564 227 6.28 %
Rwork0.1983 3385 -
obs0.2015 3612 51.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.54 Å2
Refinement stepCycle: LAST / Resolution: 2.89→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 2 0 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036959
X-RAY DIFFRACTIONf_angle_d0.5831471
X-RAY DIFFRACTIONf_chiral_restr0.03167
X-RAY DIFFRACTIONf_plane_restr0.002642
X-RAY DIFFRACTIONf_dihedral_angle_d35.9888407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.630.2695460.1951652X-RAY DIFFRACTION19.81
3.64-34.540.25441810.19882733X-RAY DIFFRACTION82.71
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)
13.41741246101-0.6551976089040.5930687923372.751789052880.2218861305410.53115156035-0.648738957492-0.15363720076-2.967632128031.06535829832-0.1233171694721.671009374821.72626152267-0.921961709762-2.119542475822.57284220374-1.441113044860.4528044669040.9031914069230.1498464326121.6977758316-14.0801158914-14.925678903416.3666276029
26.37438090761-1.21943523634-0.6081542162635.18856728477-2.204341216023.012976036480.1352646073470.17102241406-0.547367605153-0.6644228559750.05449392738781.28301732361-0.0966112936858-1.77375316546-0.3503925678330.8548345872840.0365666526933-0.06446190900972.0887269377-0.1346627757250.856102098783-14.3388864225-4.44028643863-3.42661851626
34.40806820508-2.38187048485-2.960866160211.484725815190.572355558348.45420808181-0.4506598225451.854818315340.157393987340.509630660126-1.05043914493-0.2235892084961.220270301020.63529091285-1.951405155180.701371326372-0.39130851009-0.1077580271441.49475363436-0.08148109443190.59692182651-3.59160512418-5.765697690191.82016004931
43.16739092087-1.295579748730.1323385884745.059051334851.47214502132.642354204010.5418900280250.411244582315-0.7455354207471.87397121097-0.05746982125552.065269344641.23368327354-3.43571345538-0.8382506897061.23345560674-0.9240012626780.01107657303221.578443290870.1266834852251.56677298643-17.7401991288-9.936685197627.29193396408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 11)AA1 - 11
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 10)BB1 - 10
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 5)CC1 - 5
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 16)DD1 - 16

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