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

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Basic information

Entry
Database: PDB / ID: 6wsw
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J21 immobile Holliday junction
Components
  • DNA (5'-D(*AP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*TP*GP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*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 / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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(*AP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*TP*GP*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*AP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0807
Polymers12,7814
Non-polymers2983
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.033, 69.033, 59.371
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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DNA chain , 4 types, 4 molecules ABCD

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


Mass: 6401.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*TP*CP*A)-3')


Mass: 1504.037 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*C)-3')


Mass: 2746.809 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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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.39 Å3/Da / Density % sol: 80.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 7.0 with18 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: 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: 4917 / % possible obs: 87.3 % / Redundancy: 9.4 % / Biso Wilson estimate: 121.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 1.024 / 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
3.1-3.156.40.7691360.8250.2920.8250.4850.6
3.15-3.216.70.3011480.9830.1150.3230.55156.9
3.21-3.2780.1211760.9970.0390.1280.84159.9
3.27-3.348.20.6522120.920.2210.690.45870.2
3.34-3.4190.3992000.9810.1310.420.52873.5
3.41-3.498.60.3962260.9790.1330.4190.49775.3
3.49-3.589.10.312140.9840.1030.3270.4982
3.58-3.688.60.5812490.9640.1970.6150.46387.1
3.68-3.788.50.6122720.940.2150.6490.44292.5
3.78-3.918.90.352700.9810.120.370.52297.5
3.91-4.049.10.2722690.9860.0920.2870.5598.9
4.04-4.2110.20.232740.9890.0730.2420.598100
4.21-4.410.50.2172930.9880.0690.2280.547100
4.4-4.6310.40.1782800.9930.0570.1870.607100
4.63-4.9210.10.1252900.9920.0410.1320.934100
4.92-5.39.90.1042830.9950.0350.1091.331100
5.3-5.8310.80.0892750.9970.0280.0931.846100
5.83-6.6710.60.0842820.9960.0270.0891.928100
6.67-8.49.90.0582890.9990.0190.0612.389100
8.4-5010.10.0382790.9990.0130.042.45898.9

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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: 5KEK

5kek


Resolution: 3.12→34.517 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 47.96
RfactorNum. reflection% reflection
Rfree0.2779 489 10.16 %
Rwork0.2339 --
obs0.2381 4814 85.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 268.19 Å2 / Biso mean: 145.7309 Å2 / Biso min: 77.94 Å2
Refinement stepCycle: final / Resolution: 3.12→34.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 854 3 0 857
Biso mean--145.44 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004955
X-RAY DIFFRACTIONf_angle_d0.661465
X-RAY DIFFRACTIONf_chiral_restr0.031166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d35.413406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.12-3.57080.37691230.3389103062
3.5708-4.49730.34081730.3456160595
4.4973-34.5170.25131930.19531690100

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