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Yorodumi- PDB-6udn: Crystal Structure of a Self-Assembling DNA Scaffold Containing TA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6udn | |||||||||
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Title | Crystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and Rhombohedral Symmetry | |||||||||
Components |
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Keywords | DNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice | |||||||||
Function / homology | ARSENIC / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å | |||||||||
Authors | Simmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6udn.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6udn.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 6udn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6udn_validation.pdf.gz | 391.1 KB | Display | wwPDB validaton report |
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Full document | 6udn_full_validation.pdf.gz | 391.6 KB | Display | |
Data in XML | 6udn_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 6udn_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6udn ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udn | HTTPS FTP |
-Related structure data
Related structure data | 6u40SC 6uefC 6v6rC 6wjkC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6373.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 2754.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#4: DNA chain | Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#5: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5 mL of 0.05 M cacodylate pH 6.0 with 20 mM MgCl2, 1.0 mM spermine, 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 6933 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 94.74 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.032 / Rrim(I) all: 0.1 / Χ2: 2.659 / Net I/σ(I): 10.9 / Num. measured all: 69622 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U40 Resolution: 2.602→23.703 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 37.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 162.02 Å2 / Biso mean: 101.729 Å2 / Biso min: 54.74 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.602→23.703 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %
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