+Open data
-Basic information
Entry | Database: PDB / ID: 4ggj | ||||||
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Title | Crystal structure of Zucchini from mouse (mZuc / PLD6 / MitoPLD) | ||||||
Components | Mitochondrial cardiolipin hydrolase | ||||||
Keywords | HYDROLASE / piRNA pathway / protein-RNA interactions / piRNA RNAi / HKD motif CCCH zinc finger / nuclease / nucleic acid binding / outer mitochondrial membrane | ||||||
Function / homology | Function and homology information Synthesis of PA / cardiolipin hydrolase activity / P granule organization / RNA endonuclease activity, producing 5'-phosphomonoesters / positive regulation of mitochondrial fusion / piRNA processing / phospholipase D activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / mitochondrial fusion / spermatid development ...Synthesis of PA / cardiolipin hydrolase activity / P granule organization / RNA endonuclease activity, producing 5'-phosphomonoesters / positive regulation of mitochondrial fusion / piRNA processing / phospholipase D activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / mitochondrial fusion / spermatid development / lipid catabolic process / meiotic cell cycle / nuclear membrane / mitochondrial outer membrane / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Ipsaro, J.J. / Haase, A.D. / Hannon, G.J. / Joshua-Tor, L. | ||||||
Citation | Journal: Nature / Year: 2012 Title: The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Authors: Ipsaro, J.J. / Haase, A.D. / Knott, S.R. / Joshua-Tor, L. / Hannon, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ggj.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ggj.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ggj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/4ggj ftp://data.pdbj.org/pub/pdb/validation_reports/gg/4ggj | HTTPS FTP |
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-Related structure data
Related structure data | 4ggkC 1byrS S: Starting model for refinement C: citing same article (ref.) |
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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: 22342.830 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain, UNP residues 31-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld6 / Plasmid: pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: Q5SWZ9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#2: Chemical | ChemComp-ZN / |
#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: 31.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM Bis-Tris, pH 6.5, 18% PEG-3350, 2% tascimate, pH 6.0, 1:100 m/m ratio protein:chymotrypsin, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2012 |
Radiation | Monochromator: Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend. Second mono crystal with 4:1 magnification ratio and vertically focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 17619 / Num. obs: 17027 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BYR Resolution: 1.75→38.12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.688 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.106 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→38.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.8 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -10.386 Å / Origin y: -15.334 Å / Origin z: -12.232 Å
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Refinement TLS group |
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