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- PDB-5vy7: A self-assembling L-form DNA crystal lattice -

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Basic information

Entry
Database: PDB / ID: 5vy7
TitleA self-assembling L-form DNA crystal lattice
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
KeywordsDNA / DNA nanotechnology / self-assembly / DNA structure
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSimmons, C.R. / Yan, H.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.
Authors: Simmons, C.R. / Zhang, F. / MacCulloch, T. / Fahmi, N. / Stephanopoulos, N. / Liu, Y. / Seeman, N.C. / Yan, H.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.584, 68.584, 55.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 6466.201 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*A)-3')


Mass: 1769.193 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*GP*TP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 2129.409 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: 5.91 Å3/Da / Density % sol: 79.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM cacodylate pH 6.5, 50 mM MgCl2, 2.0 mM cobalt(III)hexamine, and 1.5 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→34.292 Å / Num. obs: 4949 / % possible obs: 86.1 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.6 / % possible all: 53.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→34.29 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 37.7
RfactorNum. reflection% reflection
Rfree0.246 259 5.23 %
Rwork0.238 --
obs0.238 4949 84.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 851 0 0 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016952
X-RAY DIFFRACTIONf_angle_d1.3321461
X-RAY DIFFRACTIONf_dihedral_angle_d39.865400
X-RAY DIFFRACTIONf_chiral_restr4.408164
X-RAY DIFFRACTIONf_plane_restr0.00742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.77940.24911160.27011948X-RAY DIFFRACTION70
3.7794-340.24471430.22912742X-RAY DIFFRACTION99

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