+Open data
-Basic information
Entry | Database: PDB / ID: 4gel | ||||||
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Title | Crystal structure of Zucchini | ||||||
Components | Mitochondrial cardiolipin hydrolase | ||||||
Keywords | HYDROLASE / piRNA / Phospholipase D / Nuclease | ||||||
Function / homology | Function and homology information Synthesis of PA / cardiolipin hydrolase activity / primary piRNA processing / oocyte karyosome formation / RNA endonuclease activity, producing 5'-phosphomonoesters / dorsal appendage formation / piRNA processing / cytoplasmic side of mitochondrial outer membrane / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulatory ncRNA-mediated gene silencing ...Synthesis of PA / cardiolipin hydrolase activity / primary piRNA processing / oocyte karyosome formation / RNA endonuclease activity, producing 5'-phosphomonoesters / dorsal appendage formation / piRNA processing / cytoplasmic side of mitochondrial outer membrane / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / regulatory ncRNA-mediated gene silencing / P granule / oogenesis / lipid catabolic process / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å | ||||||
Authors | Nishimasu, H. / Fukuhara, S. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure and function of Zucchini endoribonuclease in piRNA biogenesis Authors: Nishimasu, H. / Ishizu, H. / Saito, K. / Fukuhara, S. / Kamatani, M.K. / Bonnefond, L. / Matsumoto, N. / Nishizawa, T. / Nakanaga, K. / Aoki, J. / Ishitani, R. / Siomi, H. / Siomi, M.C. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gel.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gel.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gel ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gel | HTTPS FTP |
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-Related structure data
Related structure data | 4gemC 4genSC 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: 24799.928 Da / Num. of mol.: 2 / Fragment: DmZuc, UNP residues 41-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: zuc, CG12314 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: Q9VKD7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-EDO / #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: 2.11 Å3/Da / Density % sol: 41.83 % / Mosaicity: 0.648 ° |
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Crystal grow | Method: vapor diffusion / Details: vapor diffusion |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: May 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 39875 / % possible obs: 97.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.202 / Net I/σ(I): 10.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GEN Resolution: 1.756→42.812 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8615 / SU ML: 0.43 / σ(F): 1.47 / Phase error: 21.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.592 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.82 Å2 / Biso mean: 28.7247 Å2 / Biso min: 14.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.756→42.812 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: 14
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