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- PDB-7jj3: Self-assembly of a 3D DNA crystal lattice (4x6 scramble junction ... -

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Basic information

Entry
Database: PDB / ID: 7jj3
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 scramble junction version) containing the J16 immobile Holliday junction with R3 symmetry
Components
  • DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*GP*TP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*CP*TP*GP*TP*CP*GP*T)-3')
  • DNA (5'-D(P*CP*GP*CP*CP*GP*AP*CP*TP*C)-3')
  • DNA (5'-D(P*TP*CP*AP*GP*CP*G)-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: 2.987 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 24, 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*AP*CP*GP*AP*CP*AP*GP*TP*GP*A)-3')
B: DNA (5'-D(P*CP*GP*CP*CP*GP*AP*CP*TP*C)-3')
C: DNA (5'-D(P*TP*CP*AP*GP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*CP*TP*GP*TP*CP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1459
Polymers12,7984
Non-polymers3475
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-33 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.310, 113.310, 51.478
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 ABCD

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


Mass: 3720.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*CP*CP*GP*AP*CP*TP*C)-3')


Mass: 2676.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*AP*GP*CP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*CP*TP*GP*TP*CP*GP*T)-3')


Mass: 4591.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 5 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.: 2 / 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: 4.97 Å3/Da / Density % sol: 75.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 7.0 with 18 mM MgCl2, 2.25 mM spermine, 0.9 mM CoH18N6, and 4.5% MPD 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.987→50 Å / Num. obs: 4978 / % possible obs: 99.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 78.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.09 / Χ2: 1.367 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.057.50.6632310.8250.2360.7060.35892.8
3.05-3.117.40.3542530.9770.130.3780.40998.1
3.11-3.177.60.2012360.9950.0740.2140.51699.6
3.17-3.238.20.1052730.9960.0380.1120.682100
3.23-3.39.40.1582310.9970.0530.1670.681100
3.3-3.389.20.1132690.9960.040.120.738100
3.38-3.4690.1092320.9980.040.1160.764100
3.46-3.5610.20.1052440.9980.0350.1110.758100
3.56-3.6610.30.1372640.9970.0450.1440.763100
3.66-3.7810.10.182490.9890.0590.191.158100
3.78-3.9110.80.1592530.9930.0510.1670.871100
3.91-4.0710.70.1222390.9930.0390.1291.132100
4.07-4.2610.60.112570.9950.0360.1151.181100
4.26-4.4810.40.1142480.9940.0370.121.239100
4.48-4.7610.70.1042500.9960.0340.111.059100
4.76-5.1310.30.0912450.9930.030.0962.542100
5.13-5.649.70.072630.9960.0240.0752.192100
5.64-6.469.50.0712370.9920.0250.0761.727100
6.46-8.1310.30.0582560.9980.0190.0612.022100
8.13-5011.30.0632480.9950.0210.0665.014100

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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: 6XNA

6xna


Resolution: 2.987→35.516 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 244 5.01 %
Rwork0.1998 4625 -
obs0.2012 4869 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.92 Å2 / Biso mean: 68.5416 Å2 / Biso min: 32.63 Å2
Refinement stepCycle: final / Resolution: 2.987→35.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 854 5 0 859
Biso mean--80.56 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007953
X-RAY DIFFRACTIONf_angle_d0.9051461
X-RAY DIFFRACTIONf_chiral_restr0.047166
X-RAY DIFFRACTIONf_plane_restr0.00642
X-RAY DIFFRACTIONf_dihedral_angle_d33.711406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9872-3.76290.30071210.3004225495
3.7629-35.5160.19971230.16312371100

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