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Yorodumi- PDB-8epb: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8epb | |||||||||||||||
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Title | Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands | |||||||||||||||
Components |
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Keywords | DNA / Three-Fold Rotational Axis / Left-Handed / Parallel | |||||||||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | |||||||||||||||
Authors | Zhang, C. / Zhao, J. / Lu, B. / Sha, R. / Seeman, N.C. / Noinaj, N. / Mao, C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions. Authors: Zhang, C. / Zhao, J. / Lu, B. / Seeman, N.C. / Sha, R. / Noinaj, N. / Mao, C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8epb.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8epb.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 8epb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8epb_validation.pdf.gz | 385.4 KB | Display | wwPDB validaton report |
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Full document | 8epb_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | 8epb_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 8epb_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8epb ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8epb | HTTPS FTP |
-Related structure data
Related structure data | 8ep8C 8epdC 8epeC 8epfC 8epgC 8epiC 8f40C 8f42C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4327.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4234.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.5 ug/uL motif 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium, 0.16 M lithium sulfate monohydrate, 3 % MPD at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→32.883 Å / Num. obs: 1876 / % possible obs: 80 % / Redundancy: 7.5 % / Biso Wilson estimate: 57.95 Å2 / CC1/2: 1 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.61→2.948 Å / Num. unique obs: 208 / CC1/2: 0.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ideal B type DNA duplexes generated in Cadnano Resolution: 2.61→29.73 Å / SU ML: 0.4979 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.0368 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.58 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→29.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→29.73 Å
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Refinement TLS params. | Method: refined / Origin x: 8.67001770793 Å / Origin y: -5.50272986794 Å / Origin z: -4.96260107349 Å
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Refinement TLS group | Selection details: all |