+Open data
-Basic information
Entry | Database: PDB / ID: 3fqg | ||||||
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Title | Crystal Structure of the S. pombe Rai1 | ||||||
Components | Protein din1 | ||||||
Keywords | PROTEIN BINDING / hydrolase / mRNA processing / Nucleus / Phosphoprotein / rRNA processing / Transcription / Transcription regulation / Transcription termination | ||||||
Function / homology | Function and homology information 5'-hydroxyl dinucleotide hydrolase activity / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid metabolic process / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing ...5'-hydroxyl dinucleotide hydrolase activity / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / phosphodiesterase decapping endonuclease activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid metabolic process / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing / GDP binding / RNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Xiang, S. / Tong, L. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1. Authors: Xiang, S. / Cooper-Morgan, A. / Jiao, X. / Kiledjian, M. / Manley, J.L. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fqg.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fqg.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/3fqg ftp://data.pdbj.org/pub/pdb/validation_reports/fq/3fqg | HTTPS FTP |
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-Related structure data
-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: 41870.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: din1, Rai1, SPAC19D5.06c / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O13836 |
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#2: Chemical | ChemComp-MG / |
#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: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M sodium citrate tribasic (pH 5.0) and 20% (w/v) PEG 3350, vapor diffusion, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.981 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Mar m-165 CCD / Detector: CCD / Date: Apr 18, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 29188 / % possible obs: 97.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.332 / Net I/σ(I): 16.785 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.531 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.151 / 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 max: 125.81 Å2 / Biso mean: 27.773 Å2 / Biso min: 11.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.8046 Å / Origin y: 0.6479 Å / Origin z: 16.4782 Å
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