+Open data
-Basic information
Entry | Database: PDB / ID: 5o4p | ||||||||||||
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Title | Crystal structure of AMPylated GRP78 | ||||||||||||
Components | 78 kDa glucose-regulated protein | ||||||||||||
Keywords | ATP BINDING PROTEIN / Bip/GRP78 / AMPylation | ||||||||||||
Function / homology | Function and homology information negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process ...negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||||||||
Authors | Yan, Y. / Chen, R. / Ron, D. / Read, R. | ||||||||||||
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 | 5o4p.cif.gz | 227.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o4p.ent.gz | 177 KB | Display | PDB format |
PDBx/mmJSON format | 5o4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o4p ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o4p | HTTPS FTP |
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-Related structure data
Related structure data | 6eobC 6eocC 6eoeC 6eofC 3iucS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 28 - 548 / Label seq-ID: 2 - 522
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-Components
#1: Protein | Mass: 57494.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: G3I8R9 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5M Lithium Sulfate, 0.1M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→67.76 Å / Num. obs: 104104 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 109534 / CC1/2: 0.533 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IUC Resolution: 1.86→67.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.427 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.131 / 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: 24.866 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→67.76 Å
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Refine LS restraints |
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