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- PDB-6uef: Crystal Structure of a Self-Assembling DNA Scaffold Containing Se... -

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Basic information

Entry
Database: PDB / ID: 6uef
TitleCrystal Structure of a Self-Assembling DNA Scaffold Containing Sequence Modifications to Attempt to Disrupt Crystal Contacts in a Rhombohedral Lattice.
Components
  • DNA (5'-D(*CP*AP*AP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*GP*GP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*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*T)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 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 1.3Oct 11, 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
B: DNA (5'-D(*CP*AP*AP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*GP*GP*A)-3')
A: DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
C: DNA (5'-D(*TP*GP*TP*CP*CP*GP*AP*TP*G)-3')
D: DNA (5'-D(P*GP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,7954
Polymers12,7954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.910, 115.910, 43.988
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*AP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*GP*GP*A)-3')


Mass: 6407.161 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*CP*GP*AP*TP*G)-3')


Mass: 2746.809 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*T)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 4.44 Å3/Da / Density % sol: 72.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M TRIS pH 8.0, 200 mM MgCl2, and 15% ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock
Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 4634 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 81.21 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.03 / Rrim(I) all: 0.094 / Χ2: 2.747 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-39.10.8162250.8860.2850.8650.487100
3-3.069.80.562220.9490.1880.5910.491100
3.06-3.119.70.3242510.9820.1080.3420.61100
3.11-3.1810.40.2072270.9940.0670.2180.889100
3.18-3.2510.10.122250.9910.0420.1281.905100
3.25-3.329.90.132330.9950.0480.1391.22198.7
3.32-3.4110.30.1242310.9970.0420.1311.50998.3
3.41-3.59.90.1662200.9940.0560.1762.384100
3.5-3.6100.122410.9950.040.1271.941100
3.6-3.729.50.1472370.9930.050.1552.825100
3.72-3.859.80.1232350.9910.0410.1292.301100
3.85-410.40.1242340.9930.040.133.542100
4-4.1910.30.1112180.9960.0360.1173.782100
4.19-4.4110.10.1082340.9880.0360.1143.358100
4.41-4.68100.1042450.990.0350.113.34100
4.68-5.049.50.0952260.9910.0330.1013.775100
5.04-5.5510.30.0932350.9950.0310.0984.385100
5.55-6.3510.30.0882320.9960.0290.0924.50499.6
6.35-89.80.0792310.9960.0270.0833.822100
8-50100.0672320.9940.0230.0717.51199.6

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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: MOLECULAR REPLACEMENT
Starting model: 6U40

6u40


Resolution: 2.95→23.525 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.2559 221 4.84 %
Rwork0.2352 --
obs0.2362 4562 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.12 Å2 / Biso mean: 96.081 Å2 / Biso min: 48.8 Å2
Refinement stepCycle: final / Resolution: 2.95→23.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005956
X-RAY DIFFRACTIONf_angle_d0.7911467
X-RAY DIFFRACTIONf_chiral_restr0.043166
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d34.483406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.95-3.71180.32481120.2833212397
3.7118-23.5250.23681090.22272218100

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