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- PDB-5keo: Structure Determination of a Self-Assembling DNA Crystal -

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Basic information

Entry
Database: PDB / ID: 5keo
TitleStructure Determination of a Self-Assembling DNA Crystal
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
KeywordsDNA / Structural DNA Nanoechnology / self-assembled crystals / self-assembly
Function / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesEndothia gyrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsSimmons, C.R. / Birktoft, J.J. / Seeman, N.C. / Yan, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Construction and Structure Determination of a Three-Dimensional DNA Crystal.
Authors: Simmons, C.R. / Zhang, F. / Birktoft, J.J. / Qi, X. / Han, D. / Liu, Y. / Sha, R. / Abdallah, H.O. / Hernandez, C. / Ohayon, Y.P. / Seeman, N.C. / Yan, H.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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*CP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-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)67.946, 67.946, 58.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A)-3')


Mass: 6426.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus)
#2: DNA chain DNA (5'-D(P*CP*GP*TP*CP*A)-3')


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')


Mass: 2761.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus)
#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.) Endothia gyrosa (fungus)
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2

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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 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM cacodylate pH 6.5, 100 mM MgCl2, 1.0 mM Cobalt(III)hexamine, and 2.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.986 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 3.15→41.61 Å / Num. obs: 2899 / % possible obs: 99.7 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 71.2
Reflection shellHighest resolution: 3.15 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 19.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.15→41.61 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 147 5.08 %
Rwork0.232 --
obs0.234 2837 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 853 2 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004954
X-RAY DIFFRACTIONf_angle_d0.5881465
X-RAY DIFFRACTIONf_dihedral_angle_d35.331404
X-RAY DIFFRACTIONf_chiral_restr0.025166
X-RAY DIFFRACTIONf_plane_restr0.00342
LS refinement shellHighest resolution: 3.15 Å
RfactorNum. reflection% reflection
Rfree0.2749 144 -
Rwork0.2319 2692 -
obs--98 %

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