+Open data
-Basic information
Entry | Database: PDB / ID: 5ayk | ||||||
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Title | Crystal structure of ERdj5 form I | ||||||
Components | DnaJ homolog subfamily C member 10 | ||||||
Keywords | OXIDOREDUCTASE / PDI FAMILY / THIOREDOXIN / ENDOPLASMIC RETICULUM | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / misfolded protein binding / positive regulation of ATP-dependent activity / IRE1-mediated unfolded protein response / ATPase activator activity / protein-disulfide reductase activity ...oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / disulfide oxidoreductase activity / misfolded protein binding / positive regulation of ATP-dependent activity / IRE1-mediated unfolded protein response / ATPase activator activity / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ERAD pathway / Hsp70 protein binding / response to endoplasmic reticulum stress / negative regulation of protein phosphorylation / ATPase binding / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å | ||||||
Authors | Watanabe, S. / Maegawa, K. / Inaba, K. | ||||||
Citation | Journal: To Be Published Title: Highly dynamic nature of ERdj5 is essential for enhancement of the ER associated degradation Authors: Maegawa, K. / Watanabe, S. / Okumura, M. / Noi, K. / Inoue, M. / Ushioda, R. / Ogura, T. / Nagata, K. / Inaba, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ayk.cif.gz | 312 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayk.ent.gz | 250.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ayk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ayk_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 5ayk_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 5ayk_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 5ayk_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayk ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayk | HTTPS FTP |
-Related structure data
Related structure data | 5aylC 3apoS C: citing same article (ref.) S: Starting model for refinement |
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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: 89317.570 Da / Num. of mol.: 1 / Fragment: UNP residues 32-793 Mutation: C148S, C151S, G389V, C409S, C470S, C473S, C578S, C581S, C690S, C693S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnajc10, Erdj5, Jpdi / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami References: UniProt: Q9DC23, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor |
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#2: Chemical | ChemComp-1PS / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG8000, cystin / PH range: 7.5-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.14 Å / Num. obs: 39380 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rsym value: 0.098 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.25→2.3 Å / Mean I/σ(I) obs: 1.3 / % possible all: 94.16 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: 3APO Resolution: 2.25→19.951 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.65 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.951 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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