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- PDB-8dvw: Structure of the Campylobacter concisus glycosyltransferase PglA R203Q -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dvw | ||||||
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Title | Structure of the Campylobacter concisus glycosyltransferase PglA R203Q | ||||||
![]() | 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 | ![]() | 266.7 KB | Display | ![]() |
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PDB format | ![]() | 179.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.7 KB | Display | ![]() |
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Full document | ![]() | 759.6 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dqdC ![]() 8dvzC ![]() 6ejiS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 42013.371 Da / Num. of mol.: 1 / Mutation: R203Q 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: 3.2 Å3/Da / Density % sol: 61.58 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M BIS-TRIS pH 5.5 |
-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: Jun 18, 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: 2.29→82.21 Å / Num. obs: 23933 / % possible obs: 99 % / Redundancy: 9.8 % / Biso Wilson estimate: 48.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.089 / Rrim(I) all: 0.203 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 9.4 % / Num. unique obs: 2115 / CC1/2: 0.47 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EJI Resolution: 2.29→43.05 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8131 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: 52.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→43.05 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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