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- PDB-6wr7: Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) co... -

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Basic information

Entry
Database: PDB / ID: 6wr7
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J33 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*GP*TP*CP*A)-3')
KeywordsDNA / Structural DNA nanotechnology / immobile Holliday junctions / 3D DNA self-assembly / designer DNA crystals
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104960 United States
National Science Foundation (NSF, United States)NSF2004250 United States
CitationJournal: Nat Commun / Year: 2022
Title: The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.
Authors: Simmons, C.R. / MacCulloch, T. / Krepl, M. / Matthies, M. / Buchberger, A. / Crawford, I. / Sponer, J. / Sulc, P. / Stephanopoulos, N. / Yan, H.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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*AP*CP*TP*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')
D: DNA (5'-D(P*AP*GP*TP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,7964
Polymers12,7964
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)68.287, 68.287, 61.079
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 6441.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*GP*TP*CP*A)-3')


Mass: 1495.023 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*GP*C)-3')


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*GP*TP*CP*TP*GP*C)-3')


Mass: 2113.410 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: 6.43 Å3/Da / Density % sol: 80.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 7.0 with30 mM MgCl2, 2.5 mM spermine, and 5% PEG 400 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock
Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 5219 / % possible obs: 91.4 % / Redundancy: 8.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Χ2: 0.772 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.155.70.4121830.9240.1580.4440.43962.7
3.15-3.216.50.1392020.9940.050.1480.65274
3.21-3.276.40.1322260.9970.0480.1410.66878.2
3.27-3.346.60.1922150.9910.070.2050.53180.2
3.34-3.417.10.1672540.9940.060.1780.57483
3.41-3.497.10.2652300.9770.0980.2840.76584.9
3.49-3.587.70.2042580.9880.0720.2170.52886.3
3.58-3.687.40.5312640.8830.1950.5680.97692.3
3.68-3.788.20.5692650.9520.1980.6040.55691.4
3.78-3.918.60.442480.8690.160.4692.80195
3.91-4.048.90.3452900.9760.120.3660.47799.7
4.04-4.2110.40.2823010.990.0920.2970.482100
4.21-4.410.60.2582770.9890.0830.2710.5100
4.4-4.6310.60.1932950.9940.0620.2030.525100
4.63-4.9210.40.1372710.9940.0450.1440.58100
4.92-5.3100.0943030.9970.0310.10.682100
5.3-5.8310.90.0652750.9990.0210.0680.755100
5.83-6.6710.90.0612890.9980.0190.0650.797100
6.67-8.410.10.0452880.9990.0150.0470.959100
8.4-5010.60.0412850.9980.0140.0431.11499

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KEK

5kek


Resolution: 3.11→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.956 / SU B: 36.035 / SU ML: 0.543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.566 / ESU R Free: 0.358
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 305 5.9 %RANDOM
Rwork0.2212 ---
obs0.2239 4836 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 240.27 Å2 / Biso mean: 125.992 Å2 / Biso min: 55.69 Å2
Baniso -1Baniso -2Baniso -3
1--5.16 Å2-2.58 Å20 Å2
2---5.16 Å20 Å2
3---16.72 Å2
Refinement stepCycle: final / Resolution: 3.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Num. residues----42
LS refinement shellResolution: 3.114→3.194 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 16 -
Rwork0.477 251 -
all-267 -
obs--63.88 %

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