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Yorodumi- PDB-3nyt: X-ray crystal structure of the WlbE (WpbE) aminotransferase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nyt | ||||||
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Title | X-ray crystal structure of the WlbE (WpbE) aminotransferase from pseudomonas aeruginosa, mutation K185A, in complex with the PLP external aldimine adduct with UDP-3-amino-2-N-acetyl-glucuronic acid, at 1.3 angstrom resolution | ||||||
Components | Aminotransferase WbpE | ||||||
Keywords | TRANSFERASE / aminotransferase / PLP binding / nucleotide-sugar binding | ||||||
Function / homology | Function and homology information UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase / UDP-glucuronate biosynthetic process / O antigen biosynthetic process / polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / transaminase activity / cell wall organization / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.301 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. | ||||||
Citation | Journal: Protein Sci. / Year: 2017 Title: Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase. Authors: Dow, G.T. / Gilbert, M. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nyt.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nyt.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/3nyt ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3nyt | HTTPS FTP |
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-Related structure data
Related structure data | 3nysSC 3nyuC 5u1zC 5u20C 5u21C 5u23C 5u24C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39978.586 Da / Num. of mol.: 1 / Mutation: K185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3155, wbpE / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9HZ76 |
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#2: Chemical | ChemComp-ULP / ( |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% pentaerythritol propoxylate, 100 mM MES, 50mM UDP-3-amino-20N-acetyl-glucuronic acid, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 1, 2010 / Details: montel |
Radiation | Monochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 90696 / Num. obs: 90696 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / Num. unique all: 3399 / Rsym value: 0.33 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NYS Resolution: 1.301→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.9 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.056 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.301→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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