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Yorodumi- PDB-6e66: Crystal structure of bacterial N-acetylglucosamine transferase NleB -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+66 | ||||||
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Title | Crystal structure of bacterial N-acetylglucosamine transferase NleB | ||||||
Components | NleB | ||||||
Keywords | TRANSFERASE / NleB / Bacterial effector / Arginine GlcNAcylation | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host NF-kappaB cascade / protein-arginine N-acetylglucosaminyltransferase activity / symbiont-mediated suppression of host defense-related programmed cell death / Transferases; Glycosyltransferases; Hexosyltransferases / manganese ion binding / toxin activity / host cell cytoplasm / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Yao, Q. / Zheng, Y.Q. / Shao, F. | ||||||
Citation | Journal: Mol.Cell / Year: 2019 Title: Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Authors: Ding, J. / Pan, X. / Du, L. / Yao, Q. / Xue, J. / Yao, H. / Wang, D.C. / Li, S. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e66.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e66.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 6e66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e66 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e66 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38175.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D0NUY1, UniProt: B7UI21*PLUS |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 ammonium sulfate, 0.1 M sodium cacodylate trihydrate at pH 6.5 and 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 19964 / % possible obs: 97.94 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.439 / Num. unique obs: 1873 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→19.744 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 24.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.744 Å
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Refine LS restraints |
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LS refinement shell |
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