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

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Basic information

Entry
Database: PDB / ID: 6xdx
TitleSelf-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J6 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*AP*TP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*TP*TP*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 / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 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 11, 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*TP*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*AP*TP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0947
Polymers12,7954
Non-polymers2983
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.848, 68.848, 59.374
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*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*TP*CP*AP*CP*TP*CP*A)-3')


Mass: 2963.969 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*AP*TP*GP*TP*CP*TP*GP*C)-3')


Mass: 4920.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.35 Å3/Da / Density % sol: 80.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Cacodylate pH 6.5 with 18 mM MgCl2, 2.25 mM spermine, and 9% Isopropanol 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: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. obs: 6565 / % possible obs: 93.8 % / Redundancy: 9.8 % / Biso Wilson estimate: 76.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.044 / Rrim(I) all: 0.133 / Χ2: 4.863 / 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
2.9-2.9581.0092220.770.3541.0730.46264.5
2.95-38.50.5962520.9470.2050.6320.45370
3-3.068.20.4222520.9620.1460.4480.53572.8
3.06-3.128.10.2343060.9910.080.2470.73682.3
3.12-3.198.20.1982990.9950.0650.2091.01792
3.19-3.277.70.1033470.9960.0360.1091.69196.4
3.27-3.359.20.1343380.9820.0510.1451.193100
3.35-3.4410.40.1223600.9940.0410.1291.647100
3.44-3.5410.50.1523310.9960.0490.161.187100
3.54-3.6510.80.1353550.9960.0430.1421.28299.7
3.65-3.7810.60.1463420.9960.0470.1531.107100
3.78-3.9410.20.1233590.9920.040.1291.792100
3.94-4.119.70.1233480.9850.0410.133.76299.4
4.11-4.3310.90.1073570.9930.0340.1122.213100
4.33-4.610.80.1043460.9940.0330.1092.075100
4.6-4.9610.70.1063520.9660.0340.1113.526100
4.96-5.469.90.1043470.930.0360.117.457100
5.46-6.2411.10.0913550.9770.0290.0957.086100
6.24-7.8610.30.0933430.930.0330.09912.41100
7.86-5010.20.1383540.9460.050.14736.01999.4

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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: 2.899→29.781 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 37.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 633 9.87 %
Rwork0.2446 5779 -
obs0.246 6412 91.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.63 Å2 / Biso mean: 108.7101 Å2 / Biso min: 56.23 Å2
Refinement stepCycle: final / Resolution: 2.899→29.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 3 0 858
Biso mean--136.3 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006956
X-RAY DIFFRACTIONf_angle_d0.7661467
X-RAY DIFFRACTIONf_chiral_restr0.036166
X-RAY DIFFRACTIONf_plane_restr0.00542
X-RAY DIFFRACTIONf_dihedral_angle_d33.995406
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.899-3.12260.4583980.433993473
3.1226-3.43640.2885930.3235113089
3.4364-3.93270.31721240.30661255100
3.9327-4.95110.31191520.2821248100
4.9511-29.7810.20921660.1843121299

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