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Yorodumi- PDB-7eoi: Crystal structure of the Pepper aptamer in complex with HBC, mang... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eoi | ||||||
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Title | Crystal structure of the Pepper aptamer in complex with HBC, manganese soak | ||||||
Components | Pepper (49-MER) | ||||||
Keywords | RNA / Fluorescent RNA / Aptamer / HBC | ||||||
Function / homology | Chem-J8F / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Huang, K.Y. / Ren, A.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Structure-based investigation of fluorogenic Pepper aptamer. Authors: Huang, K. / Chen, X. / Li, C. / Song, Q. / Li, H. / Zhu, L. / Yang, Y. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eoi.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eoi.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 7eoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eoi_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7eoi_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7eoi_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 7eoi_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/7eoi ftp://data.pdbj.org/pub/pdb/validation_reports/eo/7eoi | HTTPS FTP |
-Related structure data
Related structure data | 7eogSC 7eohC 7eojC 7eokC 7eolC 7eomC 7eonC 7eooC 7eopC 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: RNA chain | Mass: 15773.372 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) Production host: in vitro transcription vector pT7-TP(deltai) (others) | ||||||
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#2: Chemical | ChemComp-J8F / | ||||||
#3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M ammonium chloride, 0.005 M magnesium chloride, 0.025 M HEPES, pH 7.0, 1.25 M 1,6-hexanediol, 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.192 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.192 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 15509 / % possible obs: 77.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.073 / Rrim(I) all: 0.188 / Χ2: 2.054 / Net I/σ(I): 3.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EOG Resolution: 1.92→35.993 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.33 / 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: 116.97 Å2 / Biso mean: 42.0224 Å2 / Biso min: 18.73 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→35.993 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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