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Open data
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Basic information
Entry | Database: PDB / ID: 6siu | ||||||||||||
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Title | Crystal structure of IbpAFic2 covalently tethered to Cdc42 | ||||||||||||
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![]() | TRANSFERASE / FIC DOMAIN / ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE / PROXIMITY ENABLED COUPLING | ||||||||||||
Function / homology | ![]() GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / AMPylase activity / positive regulation of pinocytosis / modification of synaptic structure / protein adenylyltransferase / protein adenylylation / endothelin receptor signaling pathway involved in heart process ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / AMPylase activity / positive regulation of pinocytosis / modification of synaptic structure / protein adenylyltransferase / protein adenylylation / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / negative regulation of GTPase activity / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / phagocytosis, engulfment / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOQ GTPase cycle / positive regulation of cytokinesis / Golgi organization / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phagocytic vesicle / small monomeric GTPase / G protein activity / positive regulation of DNA replication / secretory granule / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / actin filament organization / EGFR downregulation / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / cell outer membrane / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein modification process / protein localization / G beta:gamma signalling through CDC42 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gulen, B. / Roselin, M. / Albers, M. / Hedberg, C. / Itzen, A. / Pogenberg, V. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture. Authors: Gulen, B. / Rosselin, M. / Fauser, J. / Albers, M.F. / Pett, C. / Krisp, C. / Pogenberg, V. / Schluter, H. / Hedberg, C. / Itzen, A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 404.7 KB | Display | ![]() |
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PDB format | ![]() | 329.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4itrS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 35492.918 Da / Num. of mol.: 2 / Mutation: I3755C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 2336 / Gene: ibpA, p76, HSM_1489 / Production host: ![]() ![]() References: UniProt: Q06277, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 21340.635 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The ligand is the product of a bifunctional linker (TReND-1), exhibiting one chemically as well as one enzymatically reactive moiety. The chemical moiety was a thiol-reactive chloroacetamide ...Details: The ligand is the product of a bifunctional linker (TReND-1), exhibiting one chemically as well as one enzymatically reactive moiety. The chemical moiety was a thiol-reactive chloroacetamide that couple to Cys3755 (IbpA). The enzymatically reactive moiety was a tri-phosphate that transferred to the natural Tyr32 (Cdc42). This reaction resulted in the cross-linking of the two proteins. Therefore it should be covalently bonded to the S atom of Cys3755 (IbpA). Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 125 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LJN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/LJN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate and 0.1 M citric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979124 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→80.2 Å / Num. obs: 43472 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.077 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4472 / CC1/2: 0.576 / Rpim(I) all: 0.762 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ITR Resolution: 2.49→80.2 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.54 Details: Ellipsoidal anisotropic corrections were applied to the merged data using STARANISO and explain the poor completeness in the high-resolution shells.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.85 Å2 / Biso mean: 52.475 Å2 / Biso min: 13.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→80.2 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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