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Yorodumi- PDB-3uux: Crystal structure of yeast Fis1 in complex with Mdv1 fragment con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uux | ||||||
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Title | Crystal structure of yeast Fis1 in complex with Mdv1 fragment containing N-terminal extension and coiled coil domains | ||||||
Components |
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Keywords | APOPTOSIS / Tetratricopeptide repeat / mitochondrial fission / mitochondria and cytoplasm | ||||||
Function / homology | Function and homology information Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / mitochondrial genome maintenance / mitochondrial fission / positive regulation of mitochondrial fission / ubiquitin binding / peroxisome / mitochondrial outer membrane ...Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / mitochondrial genome maintenance / mitochondrial fission / positive regulation of mitochondrial fission / ubiquitin binding / peroxisome / mitochondrial outer membrane / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å | ||||||
Authors | Zhang, Y. / Chan, N.C. / Gristick, H. / Chan, D.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal structure of mitochondrial fission complex reveals scaffolding function for mitochondrial division 1 (mdv1) coiled coil. Authors: Zhang, Y. / Chan, N.C. / Ngo, H.B. / Gristick, H. / Chan, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uux.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uux.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 3uux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uux_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 3uux_full_validation.pdf.gz | 483 KB | Display | |
Data in XML | 3uux_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3uux_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/3uux ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uux | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 15128.260 Da / Num. of mol.: 2 / Fragment: cytoplasmic portion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: FIS1, MDV2, YIL065C / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P40515 #2: Protein | Mass: 27143.021 Da / Num. of mol.: 2 / Fragment: N-terminal extension and coiled coil / Mutation: K215A, K216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: MDV1, FIS2, GAG3, NET2, YJL112W, J0802 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P47025 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.54M sodium citrate, 0.1M cacodylate, 4% acetonitrile, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.896→123.514 Å / Num. all: 11999 / Num. obs: 11999 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.5 % / Rsym value: 0.076 / Net I/σ(I): 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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 / Resolution: 3.9→123.51 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2503 / WRfactor Rwork: 0.2399 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7906 / SU B: 37.203 / SU ML: 0.517 / SU Rfree: 0.7063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT; IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.89 Å2 / Biso mean: 126.7367 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.9→123.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.03
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LS refinement shell | Resolution: 3.896→3.997 Å / Total num. of bins used: 20
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