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- PDB-3nyu: X-ray crystal structure of the Wbpe (WlbE) aminotransferase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nyu | ||||||
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Title | X-ray crystal structure of the Wbpe (WlbE) aminotransferase from pseudomonas aeruginosa as the PLP internal aldimine adduct with lysine 185 | ||||||
![]() | Aminotransferase WbpE | ||||||
![]() | TRANSFERASE / aminotransferase / PLP binding / nucleotide-sugar binding | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holden, H.M. / Thoden, J.B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.1 KB | Display | ![]() |
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PDB format | ![]() | 251.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.3 KB | Display | ![]() |
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Full document | ![]() | 503.4 KB | Display | |
Data in XML | ![]() | 69.4 KB | Display | |
Data in CIF | ![]() | 102 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nysSC ![]() 3nytC ![]() 5u1zC ![]() 5u20C ![]() 5u21C ![]() 5u23C ![]() 5u24C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40264.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% pentaerythritol propoxylate, 100 mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 200622 / Num. obs: 200622 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 10.2 / Num. unique all: 9398 / Rsym value: 0.09 / % possible all: 87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NYS Resolution: 1.501→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.339 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.088 / 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: 16.789 Å2
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Refinement step | Cycle: LAST / Resolution: 1.501→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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