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

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Basic information

Entry
Database: PDB / ID: 7jkk
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J10 immobile Holliday junction with R3 symmetry
Components
  • DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*TP*GP*AP*CP*GP*TP*CP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*G)-3')
  • DNA (5'-D(P*AP*CP*GP*TP*CP*A)-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 / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 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*TP*GP*AP*CP*GP*TP*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*AP*CP*GP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0078
Polymers12,7974
Non-polymers2104
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-22 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.078, 113.078, 52.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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DNA chain , 4 types, 4 molecules BCDA

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


Mass: 6417.163 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*AP*CP*GP*TP*CP*A)-3')


Mass: 1793.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2

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Details

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: 75.46 %
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.794→50 Å / Num. obs: 6150 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 97.25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Χ2: 6.759 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.859.41.1243190.6620.3881.1910.61100
2.85-2.99.80.8043130.7790.270.8490.587100
2.9-2.969.90.7333080.8370.2450.7730.749100
2.96-3.029.50.6062940.8920.2080.6410.867100
3.02-3.0810.20.43280.9420.1310.4211.571100
3.08-3.1510.30.2852880.970.0930.35.126100
3.15-3.2310.40.2413180.9830.0820.2557.55898.5
3.23-3.3210.70.2372840.9890.0770.2498.08798.6
3.32-3.4210.50.2183120.9710.0720.239.54497.2
3.42-3.5310.20.2193140.9730.0720.23111.261100
3.53-3.659.70.1983030.9820.0670.2099.967100
3.65-3.8100.1953000.9770.0650.2058.824100
3.8-3.9710.40.1723150.9820.0560.1818.44100
3.97-4.1810.70.1543060.9870.050.16210.452100
4.18-4.4410.60.153020.980.0490.15810.376100
4.44-4.7910.30.1393060.9810.0450.1468.571100
4.79-5.2710.20.1213190.990.0390.1278.926100
5.27-6.03110.1023010.9930.0320.1078.16100
6.03-7.5910.60.0953100.9950.0310.16.85100
7.59-5010.50.0793100.990.0270.0847.0399.7

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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: 2.794→46.017 Å / SU ML: 0.77 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 38.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 607 9.94 %
Rwork0.2302 5500 -
obs0.233 6107 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.47 Å2 / Biso mean: 84.4515 Å2 / Biso min: 51.96 Å2
Refinement stepCycle: final / Resolution: 2.794→46.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 4 0 859
Biso mean--112.38 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7291467
X-RAY DIFFRACTIONf_chiral_restr0.038166
X-RAY DIFFRACTIONf_plane_restr0.00342
X-RAY DIFFRACTIONf_dihedral_angle_d35.693406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.794-3.07480.59881570.53781405100
3.0748-3.51950.29951470.2833133096
3.5195-4.43370.30921500.26291374100
4.4337-46.0170.19231530.17391391100

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