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Yorodumi- PDB-5tyh: PglD from Campylobacter jejuni NCTC 11168 in complex with 5-(2-fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tyh | ||||||
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Title | PglD from Campylobacter jejuni NCTC 11168 in complex with 5-(2-furanyl)-1H-pyrazole-3-carboxylic acid | ||||||
Components | UDP-N-acetylbacillosamine N-acetyltransferase | ||||||
Keywords | transferase/transferase inhibitor / Acetyltransferase Bacterial N-glycan biosynthesis Inhibitor Fragment-based discovery / TRANSFERASE / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information UDP-N-acetylbacillosamine N-acetyltransferase / protein N-linked glycosylation via asparagine / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Morrison, J.P. / Imperiali, B. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni. Authors: De Schutter, J.W. / Morrison, J.P. / Morrison, M.J. / Ciulli, A. / Imperiali, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tyh.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tyh.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/5tyh ftp://data.pdbj.org/pub/pdb/validation_reports/ty/5tyh | HTTPS FTP |
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-Related structure data
Related structure data | 5t2yC 2npoS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 21389.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: pglD, Cj1123c / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) References: UniProt: Q0P9D1, UDP-N-acetylbacillosamine N-acetyltransferase | ||
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#2: Chemical | #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: 3.33 Å3/Da / Density % sol: 63.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, 0.1 mM sodium acetate, 1.9 M ammonium sulphate, 22 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 16473 / % possible obs: 97.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.102→2.155 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.3 / % possible all: 83.11 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NPO Resolution: 2.1→12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.58 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.162 / 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: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.668 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→12 Å
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Refine LS restraints |
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