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- PDB-9bgr: X-ray structure of the aminotransferase from Vibrio vulnificus re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9bgr | ||||||
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Title | X-ray structure of the aminotransferase from Vibrio vulnificus responsible for the biosynthesis of 2,3-diacetamido-4-amino-2,3,4-trideoxy-arabinose in the presence of its external aldimine with 2,3-diacetamido-4-amino-2,3,4-trideoxy-l-arabinose | ||||||
![]() | aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / lipopolysaccharide / pyridoxal 5'-phosphate / 2 / 3 / 4-triacetamido-2 / 4-trideoxy-L-arabinose / Vibrio vulnificus | ||||||
Function / homology | : / TRIETHYLENE GLYCOL![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fait, D.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical Investigation of an Aminotransferase Required for the Production of 2,3,4-triacetamido-2,3,4-trideoxy-L-arabinose Authors: Fait, D.J. / Bockhaus, N.J. / Dunsirn, M.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 | ![]() | 349.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 62.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9bgpC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41880.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 976 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | Mass: 849.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H38N5O21P3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: protein incubated with 5.0 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose and 1.0 mM PLP. Precipitant: 15-20% (w/v) poly(ethylene glycol) 5000, 200 mM NaCl, and 100 mM MES (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Feb 23, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. obs: 330200 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Redundancy: 4.6 % / Rsym value: 0.087 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.05→1.15 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 73676 / Rsym value: 0.481 / % possible all: 87.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 8.476 Å2
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Refinement step | Cycle: 1 / Resolution: 1.05→38.96 Å
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Refine LS restraints |
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