[English] 日本語
Yorodumi- PDB-4rwu: J-domain of Sis1 protein, Hsp40 co-chaperone from Saccharomyces c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rwu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | J-domain of Sis1 protein, Hsp40 co-chaperone from Saccharomyces cerevisiae | |||||||||
Components | Protein SIS1 | |||||||||
Keywords | CHAPERONE / hsp40 / J-domain / cochaperone / structural genomics / APC90055.5 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | Function and homology information detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding / cellular response to starvation / translational initiation / unfolded protein binding ...detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding / cellular response to starvation / translational initiation / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / cytosolic small ribosomal subunit / nucleolus / DNA binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Osipiuk, J. / Zhou, M. / Gu, M. / Sahi, C. / Craig, E.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1. Authors: Yu, H.Y. / Ziegelhoffer, T. / Osipiuk, J. / Ciesielski, S.J. / Baranowski, M. / Zhou, M. / Joachimiak, A. / Craig, E.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rwu.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rwu.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 4rwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwu ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwu | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dmxS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9918.003 Da / Num. of mol.: 1 / Fragment: J-domain (UNP residues 1-89) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288C / Gene: N2879, SIS1, YNL007C / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25294 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.02 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→26.2 Å / Num. all: 23934 / Num. obs: 23934 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.048 / Χ2: 0.975 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DMX Resolution: 1.25→26.2 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.324 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 60.92 Å2 / Biso mean: 15.937 Å2 / Biso min: 7.48 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→26.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
|