+Open data
-Basic information
Entry | Database: PDB / ID: 4gen | ||||||
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Title | Crystal structure of Zucchini (monomer) | ||||||
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 / MAD / Resolution: 2.2 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 | 4gen.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gen.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gen_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 4gen_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 4gen_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 4gen_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/4gen ftp://data.pdbj.org/pub/pdb/validation_reports/ge/4gen | HTTPS FTP |
-Related 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: 19348.615 Da / Num. of mol.: 1 / Fragment: DmZuc UNP residues 89-250 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 |
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#2: Chemical | ChemComp-CL / |
#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: 1.8 Å3/Da / Density % sol: 31.29 % / Mosaicity: 0.871 ° |
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Crystal grow | Method: vapor diffusion / Details: vapor diffusion |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9793, 0.9800 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: Dec 7, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 6839 / % possible obs: 97.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.097 / Χ2: 1.884 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→37.48 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8077 / SU ML: 0.63 / σ(F): 1.49 / Phase error: 26.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.372 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.24 Å2 / Biso mean: 38.8704 Å2 / Biso min: 6.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→37.48 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: 2
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Refinement TLS params. | Method: refined / Origin x: -20.2294 Å / Origin y: -57.4839 Å / Origin z: -12.266 Å
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Refinement TLS group |
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