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- PDB-5i36: Crystal structure of color device state A -

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Basic information

Entry
Database: PDB / ID: 5i36
TitleCrystal structure of color device state A
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')
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: 5.123 Å
AuthorsHao, Y. / Kristiansen, M. / Sha, R. / Birktoft, J. / Mao, C. / 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 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Aug 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 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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')


Theoretical massNumber of molelcules
Total (without water)40,1577
Polymers40,1577
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-7 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.530, 69.131, 70.106
Angle α, β, γ (deg.)98.19, 97.34, 99.74
Int Tables number1
Space group name H-MP1

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Components

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DNA chain , 7 types, 7 molecules ABCDEFG

#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)

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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: 7.85 Å3/Da / Density % sol: 84.34 %
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: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 5.1→33.6 Å / Num. obs: 4725 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.902 / Net I/σ(I): 9.77
Reflection shellResolution: 5.24→5.33 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIX(1.10_2152)phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBI

3gbi


Resolution: 5.123→33.583 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.04
RfactorNum. reflection% reflection
Rfree0.165 464 9.85 %
Rwork0.1341 --
obs0.1371 4711 96.18 %
all-4711 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.123→33.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2664 0 0 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132984
X-RAY DIFFRACTIONf_angle_d1.2784593
X-RAY DIFFRACTIONf_dihedral_angle_d42.0761282
X-RAY DIFFRACTIONf_chiral_restr0.067517
X-RAY DIFFRACTIONf_plane_restr0.006131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.1228-5.86070.35521470.27751353X-RAY DIFFRACTION92
5.8607-7.3710.30231560.25851460X-RAY DIFFRACTION100
7.371-33.58390.11511610.08591434X-RAY DIFFRACTION97

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