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Yorodumi- PDB-8epe: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8epe | |||||||||||||||
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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 / Four-Fold Rotational Axis / Left-Handed / Parallel | |||||||||||||||
Function / homology | DNA Function and homology information | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 8epe.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8epe.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 8epe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8epe_validation.pdf.gz | 359.4 KB | Display | wwPDB validaton report |
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Full document | 8epe_full_validation.pdf.gz | 359.4 KB | Display | |
Data in XML | 8epe_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 8epe_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8epe ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8epe | HTTPS FTP |
-Related structure data
Related structure data | 8ep8C 8epbC 8epdC 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: 1865.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 1505.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1440.976 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: 3.32 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.5 ug/uL motif 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium pH 7.0, 0.16 M lithium sulfate monohydrate, 4 % MPD at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→34.92 Å / Num. obs: 1381 / % possible obs: 85 % / Redundancy: 10.7 % / CC1/2: 1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.45→2.995 Å / Redundancy: 9.6 % / Num. unique obs: 197 / CC1/2: 0.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ideal B type DNA duplexes generated in Cadnano Resolution: 2.45→34.92 Å / SU ML: 0.5195 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8862 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: 60.32 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→34.92 Å
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Refinement TLS params. | Method: refined / Origin x: 7.4048944634 Å / Origin y: 10.3426260165 Å / Origin z: 6.54462150541 Å
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Refinement TLS group | Selection details: all |