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- PDB-5eos: Crystallizing Strained DNA: Self-Assembly of 3D Crystals Containi... -

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Entry
Database: PDB / ID: 5eos
TitleCrystallizing Strained DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component
Components
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
KeywordsDNA / DNA nanotechnology / torsionally strained DNA / DNA lattices
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.7 Å
AuthorsHernandez, C. / Birktoft, J.J. / Seeman, N.C.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.
Authors: Hernandez, C. / Birktoft, J.J. / Ohayon, Y.P. / Chandrasekaran, A.R. / Abdallah, H. / Sha, R. / Stojanoff, V. / Mao, C. / Seeman, N.C.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.classification
Revision 1.2Jun 24, 2020Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn / struct_conn_type
Revision 1.3Mar 6, 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*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1
A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)110.011, 110.011, 83.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsThe asymmetric unit is comprised of the first 11 nucleotides of the full #1 strand (chain A), by the last 10 residues of the full #1 strand (chain C), by the first 8 nucleotides of the #2 strand (chain D) and by #3 strand (chain B). Chains A (First 11 residues of strand #1) and C (next 10 residues of strand #1) together form the first DNA strand (#1) of the experiment. This DNA strand spans two asymmetric units-hence it was divided into the current chains A and C for convenient representation and crystallographic computing. Chain A (1_555) is covalently linked to chain C of another asymmetric unit (3_555); and chain C (1_555) is covalently linked to chain A of another asymmetric unit (2_555). The #2 strand form a circular DNA molecule as a consequence of internal 3-fold symmetry of the triangle chain D in the asymmetric unit represents one of these repeating units. It has 3 symmetric and sequential repeating units that are covalently linked to each other via the O3' end of residue 13D to the O5' end of residue 6D; chain D (1_555) is covalently linked to chain D of two neighboring asymmetric units (2_555) and (3_555). The selection of residues from the DNA #2 and #3 are dictated by their proximity (base pairing) to chains A and C. Chain B in the asymmetric unit represents the third of these repeating units.

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Components

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


Mass: 3414.234 Da / Num. of mol.: 1
Fragment: The first 11 residues the DNA molecule used in the experiment
Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')


Mass: 2371.582 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*CP*TP*GP*C)-3')


Mass: 3973.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 3038.020 Da / Num. of mol.: 1
Fragment: The second 10 residues the DNA molecule used in the experiment
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: 2.34 Å3/Da / Density % sol: 64.6 % / Description: rhombohedral
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Grown by vapor diffusion while treated with a controlled temperature gradient from 333 degs to 277 degs. Ammonium Sulfate, magnesium chloride, Na Cacodylate, magnesium acetate, TRIS
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1, 1.7
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.71
ReflectionResolution: 4.7→27.5 Å / Num. obs: 4338 / % possible obs: 95 % / Redundancy: 1.8 % / Net I/σ(I): 2.6
Reflection shellResolution: 4.75→4.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 2 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 4.7→27.5 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 46.89
RfactorNum. reflection% reflection
Rfree0.2101 433 9.98 %
Rwork0.19 --
obs0.1924 4338 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 371.51 Å2 / Biso mean: 317.8413 Å2 / Biso min: 272.89 Å2
Refinement stepCycle: final / Resolution: 4.7→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 0 0 858
Num. residues----42

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