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Yorodumi- PDB-1m8v: Structure of Pyrococcus abyssii Sm Protein in Complex with a Urid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m8v | ||||||
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Title | Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Protein-RNA complex / Sm protein / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information Sm-like protein family complex / intracellular organelle / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Thore, S. / Mayer, C. / Sauter, C. / Weeks, S. / Suck, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya Authors: Thore, S. / Mayer, C. / Sauter, C. / Weeks, S. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m8v.cif.gz | 241.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m8v.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 1m8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/1m8v ftp://data.pdbj.org/pub/pdb/validation_reports/m8/1m8v | HTTPS FTP |
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-Related structure data
Related structure data | 1h64SC 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: 2098.203 Da / Num. of mol.: 7 / Source method: obtained synthetically #2: Protein | Mass: 8630.029 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Organelle (production host): PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9V0Y8 #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-U / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, Imidazole pH8.0, Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K |
Components of the solutions | Name: PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 40961 / Num. obs: 37089 / % possible obs: 90.5 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 29.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1H64 Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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