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- PDB-6u40: Crystal Structure of a Self-Assembling DNA Crystal Scaffold with ... -

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Basic information

Entry
Database: PDB / ID: 6u40
TitleCrystal Structure of a Self-Assembling DNA Crystal Scaffold with Rhombohedral Symmetry
Components
  • DNA (5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*G)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold
Function / homologyCACODYLATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Authors: Simmons, C.R. / MacCulloch, T. / Zhang, F. / Liu, Y. / Stephanopoulos, N. / Yan, H.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
A: DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
C: DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0696
Polymers12,7954
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)115.556, 115.556, 44.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 6358.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')


Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*G)-3')


Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*AP*G)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
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: 4.48 Å3/Da / Density % sol: 72.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM Cacodylate pH 7.0, 20 mM MgCl2, 1 mM Spermine, 1 mM Cobalt hexamine, 15% EtOH
Temp details: Temperature gradient generated from 60-25 degrees for 0.3 degrees/hr.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 15, 2018
RadiationMonochromator: Double crystal si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6039 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 79.11 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 2.971 / Net I/σ(I): 11.7 / Num. measured all: 61013
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.80.5326320.8250.3110.6190.484100
2.75-2.84.20.5056200.8360.2720.5750.56899.4
2.8-2.854.30.4386120.8920.2340.4970.62398.7
2.85-2.914.90.3286560.9320.1640.3670.62100
2.91-2.974.90.226150.9610.1090.2460.71999.8
2.97-3.0450.1736120.9860.0850.1930.898.7
3.04-3.125.20.126320.9910.0580.1331.008100
3.12-3.250.0936500.9950.0450.1041.477100
3.2-3.34.90.0726080.9960.0360.082.58799.7
3.3-3.44.80.0725880.9960.0370.0812.265100
3.4-3.524.80.1066500.9920.0550.124.57699.7
3.52-3.665.20.1046300.9630.0510.1164.005100
3.66-3.835.20.0886340.9930.0430.0982.83599.7
3.83-4.035.20.0886180.9880.0430.0983.807100
4.03-4.2950.076200.9930.0340.0783.178100
4.29-4.624.80.0756460.9930.0380.0854.3100
4.62-5.085.20.0746180.9940.0360.0824.399100
5.08-5.815.20.0756160.9930.0360.0835.508100
5.81-7.324.90.0766360.9940.0380.0857.198100
7.32-505.10.0576210.9970.0280.0636.56198.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.702→33.358 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 36.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 300 4.98 %
Rwork0.2388 5721 -
obs0.2396 6021 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.95 Å2 / Biso mean: 82.9716 Å2 / Biso min: 43.59 Å2
Refinement stepCycle: final / Resolution: 2.702→33.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--125.6 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7761467
X-RAY DIFFRACTIONf_chiral_restr0.041166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d36.76406
LS refinement shellResolution: 2.702→3.4035 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.353 148 -
Rwork0.2998 2835 -
obs--98 %

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