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

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Basic information

Entry
Database: PDB / ID: 6xgo
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J34 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*AP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*TP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*AP*GP*T)-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 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 17, 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*AP*AP*G)-3')
B: DNA (5'-D(P*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3')
C: DNA (5'-D(P*CP*TP*AP*GP*T)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*TP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8456
Polymers12,7964
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.810, 68.810, 59.712
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*AP*AP*G)-3')


Mass: 3416.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)-3')


Mass: 2948.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*TP*AP*GP*T)-3')


Mass: 1495.023 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*TP*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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 6.38 Å3/Da / Density % sol: 80.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M HEPES pH 7.5 with 20 mM MgCl2, 1.0 mM spermine, and 5% PEG 8000 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: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→59.59 Å / Num. obs: 6287 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.059 / Rrim(I) all: 0.144 / Χ2: 1.742 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.054.70.7472810.9150.3430.8250.51895.6
3.05-3.114.90.3183090.980.1450.3510.60396.6
3.11-3.174.90.2023000.9920.0910.2220.7997.7
3.17-3.234.80.1313300.9890.0670.1481.135100
3.23-3.350.1633220.980.0890.1871.31499.4
3.3-3.3860.163040.990.0690.1741.224100
3.38-3.465.90.1783110.9880.0840.1972.321100
3.46-3.566.20.1563300.9940.0670.171.139100
3.56-3.6660.2243160.9910.10.2451.66100
3.66-3.786.10.1813100.9880.0790.1981.379100
3.78-3.915.80.23370.990.0870.2182.393100
3.91-4.075.50.1253040.990.0580.1381.983100
4.07-4.266.30.1183270.9880.0510.1292.058100
4.26-4.486.30.1132980.9910.0480.1232.295100
4.48-4.766.20.1023330.9910.0440.1112.0699.7
4.76-5.1360.1013070.9860.0460.1112.739100
5.13-5.645.90.093320.9930.0390.0983.062100
5.64-6.466.40.0982930.9890.0410.1062.149100
6.46-8.135.90.0883190.9890.040.0972.60199.4
8.13-5060.1383240.9380.0630.1520.32998.8

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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: 6x8c

6x8c


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.963 / SU B: 13.919 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.393 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 311 5.1 %RANDOM
Rwork0.2112 ---
obs0.2124 5790 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 220.27 Å2 / Biso mean: 97.87 Å2 / Biso min: 40.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--69.07 --
Num. residues----42
LS refinement shellResolution: 3.001→3.079 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 22 -
Rwork0.336 397 -
all-419 -
obs--94.37 %

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