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

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Basic information

Entry
Database: PDB / ID: 6xfg
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J23 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*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*AP*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: 3.053 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 15, 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*G)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')
C: DNA (5'-D(P*CP*AP*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 area2680 Å2
ΔGint-13 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.458, 68.458, 60.214
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3383.224 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*AP*TP*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*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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.5 with 36 mM MgCl2, 2.25 mM spermine, and 5% PEG 400 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: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 3313 / % possible obs: 99.9 % / Redundancy: 18.7 % / Biso Wilson estimate: 87.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.013 / Rrim(I) all: 0.056 / Χ2: 0.597 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.115.90.921640.9050.2320.950.42599.4
3.1-3.1616.60.5611540.9790.1390.5790.431100
3.16-3.22180.2031660.9980.0480.2090.46100
3.22-3.2919.10.1461590.9990.0330.150.506100
3.29-3.3619.90.2141600.9970.0480.2190.481100
3.36-3.4320.20.1911580.9980.0430.1960.482100
3.43-3.5219.70.1931710.9980.0440.1980.503100
3.52-3.6220.10.1661580.9980.0370.170.525100
3.62-3.72190.191610.9940.0440.1950.506100
3.72-3.84180.141670.9970.0340.1440.498100
3.84-3.9818.90.1211610.9980.0290.1240.556100
3.98-4.1419.60.0991610.9980.0230.1020.62100
4.14-4.3319.40.0831740.9980.0190.0850.625100
4.33-4.5620.10.0771670.9990.0170.0780.601100
4.56-4.84190.0691560.9990.0160.0710.647100
4.84-5.2118.40.0531640.9990.0130.0540.731100
5.21-5.7419.10.0451730.9990.010.0460.835100
5.74-6.5719.10.04417410.010.0450.77100
6.57-8.2717.50.03817610.010.0390.849100
8.27-5016.40.0318910.0090.0320.81599

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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: 3.053→42.246 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2.07 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 161 4.95 %
Rwork0.2146 3093 -
obs0.2162 3254 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.14 Å2 / Biso mean: 99.1717 Å2 / Biso min: 54.22 Å2
Refinement stepCycle: final / Resolution: 3.053→42.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--172.95 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006956
X-RAY DIFFRACTIONf_angle_d0.8291467
X-RAY DIFFRACTIONf_chiral_restr0.039166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d36.475406
LS refinement shellResolution: 3.053→42.246 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2405 161 -
Rwork0.2146 3093 -
obs--98 %

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