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Yorodumi- PDB-4h4a: Crystal structure of the C-terminal domain of Drosophila melanoga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h4a | ||||||
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Title | Crystal structure of the C-terminal domain of Drosophila melanogaster Zucchini | ||||||
Components | Mitochondrial cardiolipin hydrolase | ||||||
Keywords | HYDROLASE / phospholipase D fold / HKD motif / nuclease/phospholipid hydrolase / nucleic acid/phospholipid | ||||||
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 / SAD / Resolution: 2.2 Å | ||||||
Authors | Voigt, F. / Schulz, E.C. / Barabas, O. | ||||||
Citation | Journal: Rna / Year: 2012 Title: Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc. Authors: Voigt, F. / Reuter, M. / Kasaruho, A. / Schulz, E.C. / Pillai, R.S. / Barabas, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h4a.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h4a.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4h4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h4a_validation.pdf.gz | 421 KB | Display | wwPDB validaton report |
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Full document | 4h4a_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 4h4a_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 4h4a_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/4h4a ftp://data.pdbj.org/pub/pdb/validation_reports/h4/4h4a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19338.666 Da / Num. of mol.: 1 / Fragment: C-terminal fragment (UNP residues 89-253) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: zuc, CG12314 / Plasmid: pETM22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9VKD7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#2: 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: 1.85 Å3/Da / Density % sol: 33.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15% PEG 3350, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97942 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012 / Details: mirrors |
Radiation | Monochromator: mirrors + Bartels monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 14007 / Num. obs: 14007 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 43.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 11.42 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1045 / Rsym value: 0.544 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→33.966 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 25.99 / 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: 64.377 Å2 / ksol: 0.387 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.303 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.966 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 27.3336 Å / Origin y: 38.5147 Å / Origin z: 6.8911 Å
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Refinement TLS group | Selection details: all |