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- PDB-8uje: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uje | ||||||
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Title | X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13 | ||||||
![]() | Glycosyl transferase | ||||||
![]() | TRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation | ||||||
Function / homology | ![]() polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation / carbohydrate binding / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Samara, N.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues. Authors: Kumar, P. / Tomita, T. / Gerken, T.A. / Ballard, C.J. / Lee, Y.S. / Weiss, L.M. / Samara, N.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.6 KB | Display | ![]() |
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PDB format | ![]() | 266.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uhvC ![]() 8uhzC ![]() 8ui1C ![]() 8ui6C ![]() 8ujfC ![]() 8ujgC ![]() 8ujhC 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
#1: Protein | Mass: 63514.129 Da / Num. of mol.: 1 / Mutation: S297G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV protease cleavage site Production host: ![]() References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase | ||||||
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#2: Chemical | ChemComp-UDP / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2022 / Details: CRL single axis focusing system |
Radiation | Monochromator: FMB OXFORD single crystal side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 24551 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 52.87 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.072 / Rrim(I) all: 0.164 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1164 / CC1/2: 0.43 / CC star: 0.775 / Rpim(I) all: 0.598 / Rrim(I) all: 1.127 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 59.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.91 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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