+Open data
-Basic information
Entry | Database: PDB / ID: 2d0j | ||||||
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Title | Crystal Structure of Human GlcAT-S Apo Form | ||||||
Components | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 | ||||||
Keywords | TRANSFERASE / Rossmann-like fold / glucuronyltransferase | ||||||
Function / homology | Function and homology information galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / A tetrasaccharide linker sequence is required for GAG synthesis / protein glycosylation / membrane => GO:0016020 / carbohydrate metabolic process / Golgi membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shiba, T. / Kakuda, S. / Ishiguro, M. / Oka, S. / Kawasaki, T. / Wakatsuki, S. / Kato, R. | ||||||
Citation | Journal: To be published Title: Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope Authors: Shiba, T. / Kakuda, S. / Ishiguro, M. / Morita, I. / Oka, S. / Kawasaki, T. / Wakatsuki, S. / Kato, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d0j.cif.gz | 208.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d0j.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d0j ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d0j | HTTPS FTP |
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-Related structure data
Related structure data | 1v82S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28234.346 Da / Num. of mol.: 4 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q9NPZ5, galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG5000 MME, di-sodium hydrogen phosphate, cesium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 79510 / Num. obs: 76289 / % possible obs: 96 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.9 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V82 Resolution: 2→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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