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

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Basic information

Entry
Database: PDB / ID: 7jki
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J7 immobile Holliday junction with R3 symmetry
Components
  • DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*AP*GP*AP*CP*GP*GP*TP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*CP*T)-3')
  • DNA (5'-D(P*GP*TP*GP*TP*CP*GP*T)-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: 3.019 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 28, 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*AP*GP*AP*CP*GP*GP*TP*GP*AP*CP*TP*C)-3')
C: DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*TP*CP*GP*T)-3')
A: DNA (5'-D(P*CP*CP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8466
Polymers12,7974
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-17 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.715, 113.715, 52.054
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*AP*GP*AP*CP*GP*GP*TP*GP*AP*CP*TP*C)-3')


Mass: 6466.201 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*A)-3')


Mass: 2426.617 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*CP*CP*GP*TP*CP*T)-3')


Mass: 1760.179 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: 5.06 Å3/Da / Density % sol: 75.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.0 with 10 mM MgCl2, 2.5 mM spermine, 5 mM CaCl2, and 10% 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: 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: 4711 / % possible obs: 95.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 103.66 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.046 / Rrim(I) all: 0.15 / Χ2: 5.774 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.057.10.7652410.8940.2620.8110.50189.6
3.05-3.117.70.3722220.9880.1220.3920.82896.1
3.11-3.178.30.2462300.9890.0790.2591.75597.9
3.17-3.238.80.2022520.9960.0660.2122.83799.6
3.23-3.39.40.2012410.990.0650.2111.892100
3.3-3.389.60.1662630.9940.0560.1752.22899.6
3.38-3.469.60.1812330.9910.0590.1912.322100
3.46-3.569.90.192580.9910.0610.22.444100
3.56-3.667.30.2891380.9770.1070.3091.89456.8
3.66-3.789.40.2921800.9710.1020.311.81673.2
3.78-3.9110.80.242450.9770.0760.2522.032100
3.91-4.0710.80.1792330.9840.0570.1873.403100
4.07-4.2610.70.1612480.9910.0510.1693.577100
4.26-4.4810.70.1572530.9880.050.1654.267100
4.48-4.7610.50.1622440.9890.0520.176.15599.2
4.76-5.1310.20.1442540.9870.0470.1517.113100
5.13-5.6410.90.1342490.990.0420.149.258100
5.64-6.4610.60.1182340.990.0380.12412.517100
6.46-8.13100.0882490.9950.0290.09213.27799.6
8.13-5010.40.1412440.9820.0460.14825.96198.4

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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: 3.019→32.827 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 236 5.13 %
Rwork0.2144 4361 -
obs0.2168 4597 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.38 Å2 / Biso mean: 106.2416 Å2 / Biso min: 60.41 Å2
Refinement stepCycle: final / Resolution: 3.019→32.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--89.76 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7091467
X-RAY DIFFRACTIONf_chiral_restr0.037166
X-RAY DIFFRACTIONf_plane_restr0.00342
X-RAY DIFFRACTIONf_dihedral_angle_d34.623406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.019-3.80230.34481120.3191203887
3.8023-32.8270.2321240.1905232399

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