+Open data
-Basic information
Entry | Database: PDB / ID: 4mix | ||||||
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Title | PaToxG Glycosyltransferase | ||||||
Components | Putative insecticidal toxin | ||||||
Keywords | TRANSFERASE / tyrosine glycosylation / UDP-GlcNAc / nucleotide-binding domain a/b/a / Rossmann-like / Glycosyltransferase / Rho-proteins | ||||||
Function / homology | Function and homology information : / protein N-acetylglucosaminyltransferase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / Transferases; Glycosyltransferases; Hexosyltransferases / regulation of GTPase activity / metabolic process / toxin activity / calcium ion binding / host cell plasma membrane ...: / protein N-acetylglucosaminyltransferase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / Transferases; Glycosyltransferases; Hexosyltransferases / regulation of GTPase activity / metabolic process / toxin activity / calcium ion binding / host cell plasma membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Photorhabdus asymbiotica subsp. asymbiotica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Bogdanovic, X. / Wirth, C. / Hunte, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: A bacterial toxin catalyzing tyrosine glycosylation of Rho and deamidation of Gq and Gi proteins. Authors: Jank, T. / Bogdanovic, X. / Wirth, C. / Haaf, E. / Spoerner, M. / Bohmer, K.E. / Steinemann, M. / Orth, J.H. / Kalbitzer, H.R. / Warscheid, B. / Hunte, C. / Aktories, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mix.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mix.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/4mix ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mix | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37702.242 Da / Num. of mol.: 2 / Fragment: UNP residues 2114-2449 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica (bacteria) Strain: ATCC 43949 / 3105-77 / Gene: PAU_02230 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* CdonPlus References: UniProt: C7BKP9, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #3: Chemical | #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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 3350, 500 mM NaCl, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator, Dynamically bendable mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57.38 Å / Num. all: 64580 / Num. obs: 64580 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.0229 / Mean I/σ(I) obs: 1.1 / Num. unique all: 9347 / Rsym value: 0.0245 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→56.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.649 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 30.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→56.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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