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- PDB-7jp9: Self-assembly of a 3D DNA crystal lattice (4x6 duplex version) co... -

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Basic information

Entry
Database: PDB / ID: 7jp9
TitleSelf-assembly of a 3D DNA crystal lattice (4x6 duplex version) containing the J8 immobile Holliday junction
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*G)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*CP*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: 3.157 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*AP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*TP*CP*GP*TP*CP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*G)-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9596
Polymers12,7974
Non-polymers1612
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.304, 68.304, 54.283
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(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')


Mass: 6435.191 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*T)-3')


Mass: 1775.190 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*G)-3')


Mass: 2457.627 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, 2 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2

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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: 5.71 Å3/Da / Density % sol: 78.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.0 with 200 mM Ca(CH3COO)2 and 2.5 M NaCl 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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 3906 / % possible obs: 80 % / Redundancy: 4.6 % / Biso Wilson estimate: 92.41 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Rrim(I) all: 0.092 / Χ2: 1.822 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.22.40.4621120.870.2790.5450.74544.3
3.2-3.262.90.2671180.930.1360.3021.57450
3.26-3.332.40.4071200.7810.240.4760.90450.2
3.33-3.393.20.2611240.9430.1330.2941.62651
3.39-3.472.90.6471550.1850.4550.88.59663.8
3.47-3.553.10.5461560.7320.3120.6330.78667.5
3.55-3.6430.7071690.7870.4080.8220.72464.8
3.64-3.733.60.5381750.4310.3020.623.03673.2
3.73-3.843.90.4141750.9080.2190.470.71872.6
3.84-3.974.10.5932180.2960.3180.6763.68783.2
3.97-4.114.40.4912050.8530.250.5530.75986.9
4.11-4.274.80.4342320.8950.2130.4850.86193.9
4.27-4.474.90.3472440.9080.1740.3890.77999.2
4.47-4.75.30.3682340.9160.1760.4090.861100
4.7-55.60.2322450.9690.1070.2561.147100
5-5.385.70.152530.9850.0690.1651.493100
5.38-5.935.80.1222370.9910.0560.1351.726100
5.93-6.785.80.0982550.9920.0450.1081.993100
6.78-8.545.60.0522350.9970.0240.0581.813100
8.54-505.80.052440.9990.0230.0553.98998.8

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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: 3.157→34.152 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 35.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 228 5.87 %
Rwork0.2569 3658 -
obs0.258 3886 79.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.9 Å2 / Biso mean: 117.9718 Å2 / Biso min: 66.73 Å2
Refinement stepCycle: final / Resolution: 3.157→34.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--135.24 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006956
X-RAY DIFFRACTIONf_angle_d0.7341467
X-RAY DIFFRACTIONf_chiral_restr0.036166
X-RAY DIFFRACTIONf_plane_restr0.00542
X-RAY DIFFRACTIONf_dihedral_angle_d35.749406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1574-3.9770.3467920.3727141862
3.977-34.1520.25831360.2324224098

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