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- PDB-8dvz: Structure of the Campylobacter concisus glycosyltransferase PglA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dvz | ||||||
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Title | Structure of the Campylobacter concisus glycosyltransferase PglA R282V variant | ||||||
![]() | N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase | ||||||
![]() | MEMBRANE PROTEIN / glycosyltransferase / UDP-GalNAc | ||||||
Function / homology | ![]() N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase / N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase activity / UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vuksanovic, N. / Clasman, J.R. / Bernstein, H.M. / Imperiali, B. / Allen, K.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Authors: Vuksanovic, N. / Clasman, J.R. / Imperiali, B. / Allen, K.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.5 KB | Display | ![]() |
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PDB format | ![]() | 183.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.7 KB | Display | ![]() |
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Full document | ![]() | 782.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dqdC ![]() 8dvwC ![]() 6ejiS S: Starting model for refinement 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 41984.371 Da / Num. of mol.: 1 / Mutation: R282V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0M4SVA9, N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase |
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#2: Chemical | ChemComp-UD2 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 0.1 M sodium malonate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→84.85 Å / Num. obs: 26101 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 45.6 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.27→2.34 Å / Redundancy: 3.9 % / Num. unique obs: 2337 / CC1/2: 0.813 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EJI Resolution: 2.27→64.9 Å / SU ML: 0.2918 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1466 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→64.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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