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- PDB-6x8c: Self-assembly of a 3D DNA crystal lattice (4x5 junction version) ... -

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Basic information

Entry
Database: PDB / ID: 6x8c
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J1 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*AP*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: 3.098 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
DepositionJun 1, 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*GP*CP*AP*GP*AP*CP*CP*TP*G)-3')
B: DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
C: DNA (5'-D(P*CP*AP*CP*GP*T)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9345
Polymers12,7974
Non-polymers1371
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.926, 67.926, 59.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3383.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')


Mass: 2997.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*AP*CP*GP*T)-3')


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*TP*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 4936.186 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.: 1 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 50 mM cacodylate pH 6.0, 20 mM MgCl2, 1.0 mM spermine, and 15% ethanol 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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.098→30 Å / Num. obs: 3041 / % possible obs: 99.4 % / Redundancy: 9.8 % / Biso Wilson estimate: 67.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Χ2: 1.907 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.1-3.1570.3421300.736193.5
3.15-3.217.60.1321481.112198
3.21-3.278.50.1161431.089198.6
3.27-3.348.90.241480.917199.3
3.34-3.41100.2021440.8731100
3.41-3.499.90.2181541.5571100
3.49-3.5810.80.1481540.9191100
3.58-3.6710.30.3451457.4331100
3.67-3.7810.80.1871571.1941100
3.78-3.910.50.2031492.6341100
3.9-4.0410.50.141451.0711100
4.04-4.2110.50.1121601.1821100
4.21-4.410.50.0851501.1071100
4.4-4.6310.40.0891511.0851100
4.63-4.9210.30.0741571.2691100
4.92-5.2910.50.0611571.7451100
5.29-5.82100.0531472.2581100
5.82-6.669.90.0581662.4521100
6.66-8.369.40.0311622.9841100
8.36-309.20.0211743.789197.8

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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: 5kek

5kek


Resolution: 3.098→29.467 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 286 10.17 %
Rwork0.2384 2526 -
obs0.2416 2812 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.07 Å2 / Biso mean: 79.8551 Å2 / Biso min: 43.6 Å2
Refinement stepCycle: final / Resolution: 3.098→29.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 1 0 856
Biso mean--153.07 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004956
X-RAY DIFFRACTIONf_angle_d0.6041467
X-RAY DIFFRACTIONf_chiral_restr0.029166
X-RAY DIFFRACTIONf_plane_restr0.00342
X-RAY DIFFRACTIONf_dihedral_angle_d36.074406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0984-3.90220.35131250.2881114586
3.9022-29.4670.24411610.2226138199

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