+Open data
-Basic information
Entry | Database: PDB / ID: 5whg | ||||||
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Title | Vms1 mitochondrial localization core | ||||||
Components | Protein VMS1 | ||||||
Keywords | DNA BINDING PROTEIN / ROS signalling / oxidative stress / mitochondrial quality control | ||||||
Function / homology | Function and homology information catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / : / RNA endonuclease activity / Hydrolases; Acting on ester bonds ...catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / : / RNA endonuclease activity / Hydrolases; Acting on ester bonds / endoplasmic reticulum membrane / mitochondrion / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Fredrickson, E.K. / Schubert, H.L. / Rutter, J. / Hill, C.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol. Cell / Year: 2017 Title: Sterol Oxidation Mediates Stress-Responsive Vms1 Translocation to Mitochondria. Authors: Nielson, J.R. / Fredrickson, E.K. / Waller, T.C. / Rendon, O.Z. / Schubert, H.L. / Lin, Z. / Hill, C.P. / Rutter, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5whg.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5whg.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 5whg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/5whg ftp://data.pdbj.org/pub/pdb/validation_reports/wh/5whg | HTTPS FTP |
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-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: 44843.703 Da / Num. of mol.: 1 / Mutation: delta 38-69 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: VMS1, YDR049W / Production host: Escherichia coli (E. coli) / References: UniProt: Q04311 |
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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: 1.99 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 286 K / Method: evaporation / pH: 8.5 Details: 22-24% PEG MME 2000, 100 mM Tris pH 8.5, and 0.2 M TMAO |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97862 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2013 / Details: Rh coated flat | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→40 Å / Num. obs: 10237 / % possible obs: 96.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 88.91 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 1.031 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→24.062 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Details: Refined against I+,SigI+, I-, SigI-
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 206.43 Å2 / Biso mean: 106.4493 Å2 / Biso min: 51.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→24.062 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 26.7007 Å / Origin y: 17.3242 Å / Origin z: 58.6358 Å
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Refinement TLS group |
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