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- PDB-6wt0: Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) co... -

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Basic information

Entry
Database: PDB / ID: 6wt0
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J25 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*GP*AP*GP*AP*CP*CP*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*CP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*T)-3')
KeywordsDNA / Structural DNA nanotechnology / immobile Holliday junctions / 3D DNA self-assembly / designer DNA crystals
Function / homology: / 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
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*GP*AP*GP*AP*CP*CP*GP*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*GP*GP*TP*CP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9166
Polymers12,7984
Non-polymers1182
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-21 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.948, 68.948, 59.418
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*GP*AP*GP*AP*CP*CP*GP*CP*AP*CP*TP*CP*A)-3')


Mass: 6451.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*GP*TP*CP*T)-3')


Mass: 1511.022 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*CP*GP*TP*CP*TP*GP*C)-3')


Mass: 2089.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
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: 6.37 Å3/Da / Density % sol: 80.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M TRIS pH 8.0 with 10 mM MgCl2, 1.0 mM CoH18N6, and 20% 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: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.106→34.474 Å / Num. obs: 5302 / % possible obs: 92.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.069 / Rrim(I) all: 0.149 / Χ2: 2.269 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.106-3.153.51.1511900.8790.6281.3660.48964.8
3.15-3.213.30.3851840.9670.2080.4390.89867.6
3.21-3.273.50.2332420.9810.1190.2621.15879.5
3.27-3.343.60.4972080.990.2630.5630.62275.9
3.34-3.413.80.5082590.940.2730.5790.60286.3
3.41-3.493.70.4582730.9640.2490.5230.58892.9
3.49-3.583.80.4122520.960.2180.4680.56494.4
3.58-3.683.80.4872810.9440.2740.5610.51196.2
3.68-3.784.11.0922700.8690.4091.1690.47598.5
3.78-3.914.70.5723010.9090.290.6430.552100
3.91-4.044.90.3592920.9570.1790.4020.643100
4.04-4.214.80.3132620.960.1580.3510.804100
4.21-4.44.80.2582870.970.130.290.791100
4.4-4.634.80.2222900.9540.1140.250.944100
4.63-4.924.30.1722960.9650.0920.1961.92999.7
4.92-5.34.30.1312830.9820.0650.1472.40499.6
5.3-5.834.90.1052700.9880.0530.1182.20699.7
5.83-6.674.90.1052930.980.0530.1183.26799.7
6.67-8.44.50.0762830.9950.0390.0866.61599.3
8.4-504.70.0862880.9360.0450.09713.90799.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KEK

5kek


Resolution: 3.106→34.474 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 517 9.97 %RANDOM
Rwork0.2473 4671 --
obs0.2488 5188 90.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.04 Å2 / Biso mean: 124.4405 Å2 / Biso min: 69.43 Å2
Refinement stepCycle: final / Resolution: 3.106→34.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--116.6 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.6681467
X-RAY DIFFRACTIONf_chiral_restr0.036166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d33.964406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.106-3.41790.3957940.317490270
3.4179-3.91190.4031330.3274123595
3.9119-4.92620.33421500.31281274100
4.9262-34.4740.19671400.1962126099

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