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

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Basic information

Entry
Database: PDB / ID: 7jle
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J23 immobile Holliday junction with R3 symmetry
Components
  • DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*AP*CP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*G)-3')
  • DNA (5'-D(P*GP*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 / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.017 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
DepositionJul 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
B: DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*AP*CP*GP*AP*CP*TP*C)-3')
C: DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*G)-3')
D: DNA (5'-D(P*GP*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)12,8707
Polymers12,7974
Non-polymers733
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-19 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.257, 114.257, 51.464
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*CP*TP*GP*AP*CP*GP*AP*CP*GP*AP*CP*TP*C)-3')


Mass: 6426.177 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*G)-3')


Mass: 2442.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*TP*CP*GP*T)-3')


Mass: 2144.420 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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: 5.05 Å3/Da / Density % sol: 75.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of0.05 M HEPES pH 7.5 with 80 mM MgCl2 and 2.5 mM spermine 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: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 4894 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 94.46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.107 / Χ2: 4.645 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.059.30.6672550.920.2250.7050.477100
3.05-3.1110.20.3782470.980.1210.3970.548100
3.11-3.1710.10.1452400.9970.0460.1520.744100
3.17-3.2310.70.1142510.9990.0350.1190.861100
3.23-3.310.60.1322250.9970.0410.1381.007100
3.3-3.3810.30.1092720.9970.0360.1151.182100
3.38-3.4610.60.1162240.9980.0370.1221.189100
3.46-3.5610.40.1212570.9960.0390.1271.806100
3.56-3.669.70.1722360.9910.0580.1812.03898.7
3.66-3.78100.1652470.9890.0550.1741.47899.6
3.78-3.9110.80.1452450.9910.0460.1521.724100
3.91-4.0710.90.1182340.9950.0370.1242.23100
4.07-4.2610.50.122590.9920.0390.1263.276100
4.26-4.4810.80.1192420.9880.0370.1243.854100
4.48-4.76100.1092410.9910.0360.1154.916100
4.76-5.13100.1112490.9910.0360.1178.6299.6
5.13-5.6411.20.0942540.9930.030.0995.477100
5.64-6.4610.80.0932320.9860.030.0979.869100
6.46-8.1310.30.0692400.9960.0220.0727.60298.4
8.13-5010.60.0992440.9890.0340.10533.07898.4

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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: 3.017→35.666 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 241 5 %
Rwork0.2037 4580 -
obs0.205 4821 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.56 Å2 / Biso mean: 92.4162 Å2 / Biso min: 54.51 Å2
Refinement stepCycle: final / Resolution: 3.017→35.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 3 0 858
Biso mean--91.01 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008956
X-RAY DIFFRACTIONf_angle_d0.8811467
X-RAY DIFFRACTIONf_chiral_restr0.046166
X-RAY DIFFRACTIONf_plane_restr0.00642
X-RAY DIFFRACTIONf_dihedral_angle_d35.248406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0174-3.80090.28391130.2712226196
3.8009-35.6660.21391280.1832231999

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