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- PDB-7jnk: Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex ve... -

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Basic information

Entry
Database: PDB / ID: 7jnk
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J33 immobile Holliday junction with R3 symmetry
Components
  • DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*TP*TP*GP*AP*CP*GP*AP*GP*GP*AP*GP*TP*C)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*AP*TP*GP*TP*CP*GP*T)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*CP*A)-3')
KeywordsDNA / Structural DNA nanotechnology / immobile Holliday junctions / 3D DNA self-assembly / designer DNA crystals
Function / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.105 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
DepositionAug 4, 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
B: DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*TP*TP*GP*AP*CP*GP*AP*GP*GP*AP*GP*TP*C)-3')
C: DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*C)-3')
D: DNA (5'-D(P*AP*TP*GP*TP*CP*GP*T)-3')
A: DNA (5'-D(P*TP*CP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1106
Polymers12,8364
Non-polymers2742
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-8 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.565, 113.565, 51.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 6521.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*C)-3')


Mass: 2402.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*GP*TP*CP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*CP*GP*TP*CP*A)-3')


Mass: 1784.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
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: 5.01 Å3/Da / Density % sol: 75.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.5 with 18 mM MgCl2, 2.25 mM spermine, and 9% isopropanol 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: Jun 15, 2019
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: 4441 / % possible obs: 98.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 83.85 Å2 / CC1/2: 0.919 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.039 / Rrim(I) all: 0.126 / Χ2: 1.72 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.156.90.5141840.9360.1910.5510.41285.6
3.15-3.217.10.1972200.9940.070.210.49993.2
3.21-3.278.30.22210.9970.070.2120.4896.1
3.27-3.348.90.2162150.9960.0730.2280.44898.6
3.34-3.419.30.1612280.9970.0540.170.50199.6
3.41-3.499.40.2132170.9950.0720.2250.514100
3.49-3.589.80.2082360.9940.0690.2190.506100
3.58-3.689.40.2872210.9870.0980.3030.558100
3.68-3.7810.10.3292260.9670.1090.3470.57100
3.78-3.9110.30.2982260.9760.0980.3140.486100
3.91-4.0410.80.1762170.9910.0560.1850.478100
4.04-4.2110.60.152250.9910.0480.1580.538100
4.21-4.410.90.1422300.9940.0450.1490.57100
4.4-4.6310.50.142240.9930.0450.1480.514100
4.63-4.92100.0962340.9970.0320.1020.568100
4.92-5.310.70.0732170.9960.0230.0760.719100
5.3-5.83110.0582220.9980.0180.0610.767100
5.83-6.6710.70.0552270.9980.0170.0570.664100
6.67-8.4100.0462270.9980.0150.0480.798100
8.4-5010.70.1252240.9810.040.13221.382100

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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: 5VY6

5vy6


Resolution: 3.105→30.201 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 32.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 438 9.98 %
Rwork0.2347 3950 -
obs0.2362 4388 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.35 Å2 / Biso mean: 78.7266 Å2 / Biso min: 52.46 Å2
Refinement stepCycle: final / Resolution: 3.105→30.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 2 0 860
Biso mean--162.18 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006960
X-RAY DIFFRACTIONf_angle_d0.6761474
X-RAY DIFFRACTIONf_chiral_restr0.033166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d33.698406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.105-3.55330.28131370.283125893
3.5533-4.47450.33521460.29151353100
4.4745-30.2010.20311550.19811339100

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