+Open data
-Basic information
Entry | Database: PDB / ID: 5diy | |||||||||
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Title | Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N | |||||||||
Components |
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Keywords | HYDROLASE / GH84 / OGA / O-GlcNAc hydrolase / O-GlcNAcase | |||||||||
Function / homology | Function and homology information cardiac septum development / coronary vasculature development / hydrolase activity, acting on glycosyl bonds / aorta development / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / enzyme activator activity / metabolic process / heart morphogenesis ...cardiac septum development / coronary vasculature development / hydrolase activity, acting on glycosyl bonds / aorta development / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / non-canonical NF-kappaB signal transduction / enzyme activator activity / metabolic process / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / lung development / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / protein-containing complex / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermobaculum terrenum (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å | |||||||||
Authors | Ostrowski, A. / Gundogdu, M. / Ferenbach, A.T. / Lebedev, A. / van Aalten, D.M.F. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum. Authors: Ostrowski, A. / Gundogdu, M. / Ferenbach, A.T. / Lebedev, A.A. / van Aalten, D.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5diy.cif.gz | 200.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5diy.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 5diy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/5diy ftp://data.pdbj.org/pub/pdb/validation_reports/di/5diy | HTTPS FTP |
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-Related 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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-Components
#1: Protein/peptide | Mass: 750.797 Da / Num. of mol.: 2 / Fragment: UNP residues 392-398 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15750 #2: Protein | Mass: 55478.367 Da / Num. of mol.: 2 / Mutation: D120N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobaculum terrenum (bacteria) / Gene: Tter_0116 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D1CDN2 #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 38% PEG-4000, 400 mM sodium acetate, 0.1 M Tris-HCl PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→49.03 Å / Num. all: 237569 / Num. obs: 57769 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Resolution: 2.06→49.03 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.992 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.189 / 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: 32.583 Å2
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Refinement step | Cycle: 1 / Resolution: 2.06→49.03 Å
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