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- PDB-6wsx: Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) co... -

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Basic information

Entry
Database: PDB / ID: 6wsx
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J22 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*CP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*G)-3')
  • DNA (5'-D(P*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-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: 3.122 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
DepositionMay 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*GP*AP*CP*GP*CP*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*G)-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,7984
Polymers12,7984
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.441, 69.441, 59.459
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*TP*GP*AP*CP*GP*CP*CP*AP*CP*TP*CP*A)-3')


Mass: 6402.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*TP*CP*A)-3')


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


Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 6.47 Å3/Da / Density % sol: 80.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.0, 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: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 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: 4852 / % possible obs: 85.1 % / Redundancy: 9.2 % / Biso Wilson estimate: 86.79 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.043 / Rrim(I) all: 0.132 / Χ2: 2.732 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.156.40.8541450.7180.3430.9240.54151.2
3.15-3.215.80.4981400.8830.1970.5371.44752.6
3.21-3.276.80.2971720.9650.1080.3173.57656.2
3.27-3.346.60.2841710.9910.1150.3080.71262.4
3.34-3.417.80.4752050.9320.1670.5041.38970.2
3.41-3.497.60.4992180.940.1750.531.26774.1
3.49-3.588.40.4942020.9090.1720.5241.2875.1
3.58-3.688.30.6472450.9150.2250.6861.27182.8
3.68-3.788.50.7682560.8490.2720.8160.6590.1
3.78-3.918.70.5082670.8810.1760.5391.23896.4
3.91-4.049.50.4122800.9430.140.4351.298100
4.04-4.2110.60.3862820.9490.1260.4071.057100
4.21-4.410.60.3272910.970.1060.3441.106100
4.4-4.6310.50.2912900.9580.0940.3051.262100
4.63-4.9210.20.2142910.9770.070.2252.1100
4.92-5.3100.1512880.990.050.1593.008100
5.3-5.8310.80.1382690.9870.0440.1455.385100
5.83-6.6710.70.1382840.980.0440.1455.234100
6.67-8.49.70.1122890.990.0390.1197.55898
8.4-509.60.0842670.9950.030.0897.47992.7

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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: 5KEK

5kek


Resolution: 3.122→34.721 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 49.66
RfactorNum. reflection% reflection
Rfree0.2563 494 10.28 %
Rwork0.2461 --
obs0.2473 4804 84.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.93 Å2 / Biso mean: 123.6319 Å2 / Biso min: 79.96 Å2
Refinement stepCycle: final / Resolution: 3.122→34.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011956
X-RAY DIFFRACTIONf_angle_d1.0721467
X-RAY DIFFRACTIONf_chiral_restr0.059166
X-RAY DIFFRACTIONf_plane_restr0.00842
X-RAY DIFFRACTIONf_dihedral_angle_d35.705406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.122-3.43570.3184780.318772056
3.4357-3.93230.35241280.3297105283
3.9323-4.9520.33061380.34581300100
4.952-34.7210.22051500.2006123898

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