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- PDB-5i6t: Crystal structure of color device state C -

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Basic information

Entry
Database: PDB / ID: 5i6t
TitleCrystal structure of color device state C
Components
  • DNA (26-MER)
  • DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3')
  • DNA (5'-D(*CP*AP*GP*AP*TP*AP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*TP*AP*CP*G)-3')
  • DNA (5'-D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3')
  • DNA (5'-D(P*TP*AP*GP*AP*C)-3')
KeywordsDNA / tensegrity triangle / single strand extending
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.283 Å
AuthorsHao, Y. / Birktoft, J. / Seeman, N.C.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-29554 United States
National Science Foundation (NSF, United States)CMMI-1120890 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)CCF-1526650 United States
Army Research OfficeMURI W911NF-11-1-0024 United States
Office of Naval ResearchMURI N000140911118 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
Gordon and Betty Moore FoundationGBMF3849 United States
CitationJournal: Nat Chem / Year: 2017
Title: A device that operates within a self-assembled 3D DNA crystal.
Authors: Hao, Y. / Kristiansen, M. / Sha, R. / Birktoft, J.J. / Hernandez, C. / Mao, C. / Seeman, N.C.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
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
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
B: DNA (26-MER)
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
D: DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3')
E: DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3')
F: DNA (5'-D(*CP*AP*GP*AP*TP*AP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*TP*AP*CP*G)-3')
G: DNA (5'-D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
H: DNA (5'-D(P*TP*AP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,6618
Polymers41,6618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint-12 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.056, 69.411, 69.858
Angle α, β, γ (deg.)98.730, 97.580, 99.270
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 8 types, 8 molecules ABCDEFGH

#1: DNA chain DNA (5'-D(*GP*TP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')


Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (26-MER)


Mass: 7853.070 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*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')


Mass: 4366.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*CP*AP*GP*TP*CP*GP*TP*GP*GP*TP*AP*TP*C)-3')


Mass: 4295.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*AP*GP*TP*GP*GP*TP*CP*GP*C)-3')


Mass: 4327.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*CP*AP*GP*AP*TP*AP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*TP*AP*CP*G)-3')


Mass: 6432.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(*GP*AP*GP*CP*GP*AP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (5'-D(P*TP*AP*GP*AP*C)-3')


Mass: 1504.037 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

CrystalDensity Matthews: 7.62 Å3/Da / Density % sol: 83.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 mM sodium cacodylate, 50 mM magnesium acetate, 50 mM ammonium sulfate, 5 mM magnesium chloride and 25 mM Tris HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.27→50 Å / Num. obs: 4417 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 270.34 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.304 / Net I/av σ(I): 29.483 / Net I/σ(I): 8.5 / Num. measured all: 16778
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
5.27-5.363.50.7282160.90296.9
5.36-5.463.70.6622030.93396.7
5.46-5.563.70.6162400.84699.2
5.56-5.683.80.5812140.82899.5
5.68-5.83.80.5672210.88699.5
5.8-5.933.80.5962150.92799.1
5.93-6.083.90.4512310.87299.6
6.08-6.253.90.5582240.99100
6.25-6.433.80.3332150.9599.5
6.43-6.643.80.3032220.8499.6
6.64-6.873.80.2392450.95799.6
6.87-7.153.80.2061960.974100
7.15-7.473.70.1442371.16599.2
7.47-7.873.80.0872131.225100
7.87-8.363.60.0682231.44299.6
8.36-93.90.0642331.579100
9-9.940.0642221.684100
9.9-11.3140.0522341.86899.6
11.31-14.23.90.0522132.711100
14.2-503.80.0492003.54190.1

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Processing

Software
NameVersionClassification
PHENIXdev_2276refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBI

3gbi


Resolution: 5.283→41.74 Å / SU ML: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 45.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 437 9.92 %
Rwork0.1553 3967 -
obs0.1606 4404 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 905.58 Å2 / Biso mean: 358.3626 Å2 / Biso min: 205.99 Å2
Refinement stepCycle: final / Resolution: 5.283→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2767 0 0 2767
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133099
X-RAY DIFFRACTIONf_angle_d1.324768
X-RAY DIFFRACTIONf_chiral_restr0.068537
X-RAY DIFFRACTIONf_plane_restr0.006136
X-RAY DIFFRACTIONf_dihedral_angle_d42.1321329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.283-6.04550.34941440.25461296144097
6.0455-7.60910.30971460.278713611507100
7.6091-41.74170.15781470.11311310145798

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