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Yorodumi- PDB-8wo8: Crystal Structure of an RNA-binding protein, FAU-1, from Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wo8 | ||||||
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Title | Crystal Structure of an RNA-binding protein, FAU-1, from Pyrococcus furiosus | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RNase E | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Kawai, G. / Okada, K. / Baba, S. / Sato, A. / Sakamoto, T. / Kanai, A. | ||||||
Funding support | 1items
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Citation | Journal: J.Biochem. / Year: 2024 Title: Homo-trimeric structure of the ribonuclease for rRNA processing, FAU-1, from Pyrococcus furiosus. Authors: Kawai, G. / Okada, K. / Baba, S. / Sato, A. / Sakamoto, T. / Kanai, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wo8.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wo8.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 8wo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wo8_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 8wo8_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 8wo8_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 8wo8_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/8wo8 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/8wo8 | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 55038.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GB:AB055587.1(The EHHHHHH at the C-tarminal is expression tag) Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: JCM 8422 (DSM 3638) / Gene: fau-1, aubA, PF0022 / Plasmid: pET-23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS References: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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#2: RNA chain | Mass: 919.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40%(v/v) PEG-300, 0.1 mM HEPES (pH 7.5), 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 17, 2008 | |||||||||||||||||||||
Radiation | Monochromator: BL38B1 at SPring-8 is equipped the SPring-8 standard double crystal monochromator (DCM) with Si (111) and a vertically bent cylindrical mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.58→50 Å / Num. obs: 22452 / % possible obs: 90.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 12 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AF-Q8U4Q7-F1-model_v4 Resolution: 2.78→30.01 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.874 / SU B: 13.134 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.488 Å2
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Refinement step | Cycle: 1 / Resolution: 2.78→30.01 Å
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Refine LS restraints |
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