+Open data
-Basic information
Entry | Database: PDB / ID: 3g0z | ||||||
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Title | Structure of S. pombe Pop2p - Zn2+ and Mn2+ bound form | ||||||
Components | CCR4-Not complex subunit Caf1 | ||||||
Keywords | Hydrolase / Gene Regulation / mRNA turnover / deadenylation / Ccr4-Not / Pop2p / Caf1p / DEDD exonuclease | ||||||
Function / homology | Function and homology information poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA nuclease activity / P-body / manganese ion binding ...poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA nuclease activity / P-body / manganese ion binding / chromatin binding / mRNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.004 Å | ||||||
Authors | Andersen, K.R. / Jonstrup, A.T. / Van, L.B. / Brodersen, D.E. | ||||||
Citation | Journal: Rna / Year: 2009 Title: The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site Authors: Andersen, K.R. / Jonstrup, A.T. / Van, L.B. / Brodersen, D.E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g0z.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g0z.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 3g0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/3g0z ftp://data.pdbj.org/pub/pdb/validation_reports/g0/3g0z | HTTPS FTP |
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-Related structure data
Related structure data | 3g10C 2p51S C: citing same article (ref.) S: Starting model for refinement |
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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: Protein | Mass: 37316.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: caf1, SPCC18.06c / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta DE3 / References: UniProt: O74856 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MN / |
#4: 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: 1.793357 Å3/Da / Density % sol: 31.41354 % / Mosaicity: 0.575 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 18% PEG 3350, 200mM sodium formate, 5mM beta-mercaptoethanol, 7.1mM MgCl2, 0.075mM MnCl2, 0.22mM ZnCl2, pH 8.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.271 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007 |
Radiation | Monochromator: Si(111) double crystal monochromator, water-cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.271 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.2 Å / Num. obs: 17779 / % possible obs: 95.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.09 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.17 / Net I/σ(I): 22.468 / Num. measured all: 259583 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3 / Num. unique all: 1398 / Χ2: 1.119 / % possible all: 76.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P51 Resolution: 2.004→47.166 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU ML: 0.09 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.19 / 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 / Bsol: 50.744 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.61 Å2 / Biso mean: 41.23 Å2 / Biso min: 22.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.004→47.166 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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