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- PDB-6dkl: Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA... -

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Basic information

Entry
Database: PDB / ID: 6dkl
TitleCrystal Structure of a Rationally Designed Six-Fold Symmetric DNA Scaffold
Components
  • DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')
KeywordsDNA / DNA Nanotechnology / Structural DNA Nanotechnology / self-assembly / crystal design / DNA crystals
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.034 Å
AuthorsSimmons, C.R. / Zhang, F. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
National Science Foundation (NSF, United States)1360635 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry.
Authors: Zhang, F. / Simmons, C.R. / Gates, J. / Liu, Y. / Yan, H.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3')
B: DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')
C: DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.408, 68.408, 143.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')


Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')


Mass: 3371.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM Cacodylate pH 6.0, 10 mM MgCl2, 200 mM sodium citrate, 5% isopropanol
Temp details: Temperature gradient was generated from 60C-25C for .3 degrees per hour.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.034→50 Å / Num. obs: 6788 / % possible obs: 91.8 % / Redundancy: 6.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 42.1
Reflection shellResolution: 3.034→3.1 Å / Num. unique obs: 252 / CC1/2: 0.93 / Rpim(I) all: 0.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.034→37.1758 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 41.42
RfactorNum. reflection% reflection
Rfree0.2339 660 10 %
Rwork0.2278 --
obs0.2284 6598 89.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.034→37.1758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 851 0 0 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008952
X-RAY DIFFRACTIONf_angle_d0.9551461
X-RAY DIFFRACTIONf_dihedral_angle_d32.543400
X-RAY DIFFRACTIONf_chiral_restr0.057164
X-RAY DIFFRACTIONf_plane_restr0.00642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0342-3.26830.3872960.3426894X-RAY DIFFRACTION67
3.2683-3.5970.28441210.24041133X-RAY DIFFRACTION84
3.597-4.11690.2891470.28851273X-RAY DIFFRACTION98
4.1169-5.18460.30821510.2881318X-RAY DIFFRACTION100
5.1846-37.1730.1811450.1891320X-RAY DIFFRACTION98

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