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

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Basic information

Entry
Database: PDB / ID: 6xdz
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J8 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*GP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*TP*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: 3.106 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 11, 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*AP*G)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')
C: DNA (5'-D(P*CP*TP*TP*GP*T)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0716
Polymers12,7974
Non-polymers2742
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-15 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.883, 68.883, 59.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 3392.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')


Mass: 2957.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*TP*GP*T)-3')


Mass: 1486.009 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*GP*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 4961.199 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.: 2 / 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: 6.41 Å3/Da / Density % sol: 80.8 %
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: APS / Beamline: 19-ID / Wavelength: 0.92 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: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 5407 / % possible obs: 94 % / Redundancy: 9.4 % / Biso Wilson estimate: 129.48 Å2 / CC star: 0.857 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Χ2: 3.289 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.157.60.7921910.8560.2790.8420.51162.2
3.15-3.217.60.3551740.9820.1240.3760.64868
3.21-3.277.40.2032610.9950.0680.2141.27383.7
3.27-3.347.70.352270.9930.1210.3710.68785.3
3.34-3.418.50.2682790.9810.0910.2830.79591.8
3.41-3.498.50.3252880.9820.110.3430.63495
3.49-3.588.70.282370.9880.0950.2960.76197.1
3.58-3.688.80.3453010.9840.1180.3660.74399
3.68-3.788.60.3832870.9780.1350.4060.6499.7
3.78-3.9110.30.2982850.9750.0970.3131.08100
3.91-4.0410.40.2353100.9850.0770.2471.143100
4.04-4.2110.60.2012580.9890.0650.2110.916100
4.21-4.410.20.1642930.9850.0540.1731.386100
4.4-4.6310.20.1552940.9850.0510.1631.678100
4.63-4.929.20.1163010.9930.0390.1232.124100
4.92-5.310.50.1022880.9870.0330.1083.516100
5.3-5.8310.50.0942690.9830.030.0994.585100
5.83-6.6710.30.0952940.9820.0310.16.865100
6.67-8.49.70.072840.9910.0230.07410.21499.6
8.4-5010.10.0872860.9840.0290.09218.87697.9

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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: 6X8C

6x8c


Resolution: 3.106→29.851 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 275 5.19 %
Rwork0.2216 5023 -
obs0.2221 5298 92.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.26 Å2 / Biso mean: 136.1655 Å2 / Biso min: 74.83 Å2
Refinement stepCycle: final / Resolution: 3.106→29.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--161.33 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.6411467
X-RAY DIFFRACTIONf_chiral_restr0.031166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d35.044406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.106-3.91170.3441140.3516232385
3.9117-29.8510.21391610.19752700100

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