+Open data
-Basic information
Entry | Database: PDB / ID: 8ydc | |||||||||
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Title | Crystal structure of a hammerhead ribozyme with pseudoknot | |||||||||
Components |
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Keywords | RNA / catalysis | |||||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å | |||||||||
Authors | Liu, Y. / Zhan, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme. Authors: Zhan, X. / Wilson, T.J. / Li, Z. / Zhang, J. / Yang, Y. / Lilley, D.M.J. / Liu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ydc.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ydc.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ydc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/8ydc ftp://data.pdbj.org/pub/pdb/validation_reports/yd/8ydc | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 18715.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (code 3) (others) |
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#2: DNA/RNA hybrid | Mass: 4447.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
#3: Chemical | ChemComp-GTP / |
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: 5.51 Å3/Da / Density % sol: 77.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: Magnesium acetate tetrahydrate MES monohydrate Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→16.25 Å / Num. obs: 12665 / % possible obs: 98.38 % / Redundancy: 37.8 % / CC1/2: 1 / Net I/σ(I): 18.05 |
Reflection shell | Resolution: 2.89→2.993 Å / Num. unique obs: 1226 / CC1/2: 0.866 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.89→16.25 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / 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 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→16.25 Å
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Refine LS restraints |
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LS refinement shell |
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