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- PDB-6i7l: Crystal structure of monomeric FICD mutant L258D complexed with M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i7l | |||||||||||||||
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Title | Crystal structure of monomeric FICD mutant L258D complexed with MgAMP-PNP | |||||||||||||||
![]() | Adenosine monophosphate-protein transferase FICD | |||||||||||||||
![]() | TRANSFERASE / Fic / AMPylation / UPR / BiP | |||||||||||||||
Function / homology | ![]() protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding ...protein deadenylylation / protein adenylylhydrolase activity / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of IRE1-mediated unfolded protein response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / negative regulation of GTPase activity / response to unfolded protein / Hsp70 protein binding / response to endoplasmic reticulum stress / protein-folding chaperone binding / endoplasmic reticulum membrane / protein homodimerization activity / ATP binding / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Perera, L.A. / Yan, Y. / Read, R.J. / Ron, D. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP. Authors: Perera, L.A. / Rato, C. / Yan, Y. / Neidhardt, L. / McLaughlin, S.H. / Read, R.J. / Preissler, S. / Ron, D. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 65 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 770.7 KB | Display | ![]() |
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Full document | ![]() | 771.7 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i7gC ![]() 6i7hC ![]() 6i7iC ![]() 6i7jC ![]() 6i7kC ![]() 4u0uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39451.051 Da / Num. of mol.: 1 / Mutation: L258D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BVA6, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#2: Chemical | ChemComp-ANP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.95 Å3/Da / Density % sol: 75.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Sodium Chloride; 10% Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→93.18 Å / Num. obs: 34573 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.054 / Rrim(I) all: 0.089 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3351 / CC1/2: 0.523 / Rpim(I) all: 0.465 / Rrim(I) all: 0.771 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4u0u Resolution: 2.32→93.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.373 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.459 Å2
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Refinement step | Cycle: 1 / Resolution: 2.32→93.18 Å
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Refine LS restraints |
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