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- PDB-7jpb: Self-assembly of a 3D DNA crystal lattice (4x6 duplex version) co... -

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Basic information

Entry
Database: PDB / ID: 7jpb
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 duplex version) containing the J2 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*GP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*CP*A)-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: 3.158 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
DepositionAug 7, 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*AP*GP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*TP*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*C)-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0716
Polymers12,7974
Non-polymers2742
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.111, 69.111, 56.404
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*AP*GP*AP*CP*TP*CP*A)-3')


Mass: 6466.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*CP*GP*TP*CP*A)-3')


Mass: 1784.204 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*C)-3')


Mass: 2417.603 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)
#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: 6.08 Å3/Da / Density % sol: 79.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.5 with 2.0 mM spermine, 1.0 mM CoH18N6, and 80 mM CaCl2 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / 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: 3.15→50 Å / Num. obs: 4138 / % possible obs: 80.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 84.71 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Χ2: 1.197 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.23.20.321980.960.1620.3610.61841.5
3.2-3.263.80.1861240.9840.0920.2081.05347.7
3.26-3.333.40.2041320.9920.1070.2311.21850
3.33-3.3940.2321420.960.1060.2561.08155
3.39-3.474.60.2171500.9790.0960.2380.91558.8
3.47-3.554.50.2971660.9660.1330.3270.79361.5
3.55-3.645.60.2711650.9620.1130.2940.82766
3.64-3.735.30.3691890.9580.1560.4020.68572.4
3.73-3.845.90.3822060.9530.1530.4130.57779.2
3.84-3.9760.3492100.9530.1370.3760.75481.4
3.97-4.116.40.3372400.9590.1320.3620.86391.6
4.11-4.276.80.2952470.9720.1130.3160.93396.1
4.27-4.476.60.2832590.9560.110.3040.96398.9
4.47-4.76.90.2982640.9550.1190.3220.973100
4.7-57.80.2312540.9820.0870.2471.472100
5-5.388.60.1732410.9850.0620.1841.549100
5.38-5.939.10.1412690.9880.0510.151.676100
5.93-6.7890.1222550.9950.0440.131.7100
6.78-8.5480.1042710.9890.0420.1121.441100
8.54-508.10.0972560.9650.0410.1061.32100

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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: 5VY6

5vy6


Resolution: 3.158→34.556 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 33.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 203 4.95 %
Rwork0.2236 3894 -
obs0.2248 4097 79.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.26 Å2 / Biso mean: 129.3898 Å2 / Biso min: 74.7 Å2
Refinement stepCycle: final / Resolution: 3.158→34.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--189.79 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7551467
X-RAY DIFFRACTIONf_chiral_restr0.044166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d34.157406
LS refinement shellHighest resolution: 3.158 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2439 203 -
Rwork0.2236 3894 -
obs--80 %

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