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Yorodumi- PDB-6eoc: Crystal structure of AMPylated GRP78 in apo form (Crystal form 2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eoc | ||||||||||||
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Title | Crystal structure of AMPylated GRP78 in apo form (Crystal form 2) | ||||||||||||
Components | 78 kDa glucose-regulated protein | ||||||||||||
Keywords | CHAPERONE / GRP78 / BIP / AMPylation / apo | ||||||||||||
Function / homology | Function and homology information negative regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ATP-dependent protein folding chaperone / melanosome / endoplasmic reticulum lumen ...negative regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ATP-dependent protein folding chaperone / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||||||||
Authors | Yan, Y. / Preissler, S. / Ron, D. / Read, R.J. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Elife / Year: 2017 Title: AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation. Authors: Preissler, S. / Rohland, L. / Yan, Y. / Chen, R. / Read, R.J. / Ron, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eoc.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eoc.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 6eoc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eoc_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 6eoc_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 6eoc_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 6eoc_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eoc ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eoc | HTTPS FTP |
-Related structure data
Related structure data | 5o4pSC 6eobC 6eoeC 6eofC 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: 57407.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SO4, CITRATE / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Production host: Escherichia coli (E. coli) / References: UniProt: G3I8R9 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FLC / |
#4: 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: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 5% PEG1000, 0.1M Na2HPO4-Citrate, ph4.2, 0.2M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→75.41 Å / Num. obs: 59490 / % possible obs: 98.3 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2986 / CC1/2: 0.888 / Rpim(I) all: 0.464 / Rrim(I) all: 0.861 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O4P Resolution: 1.67→59.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.498 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.139 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→59.83 Å
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