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Yorodumi- PDB-1v84: Crystal structure of human GlcAT-P in complex with N-acetyllactos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v84 | |||||||||
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Title | Crystal structure of human GlcAT-P in complex with N-acetyllactosamine, Udp, and Mn2+ | |||||||||
Components | Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1 | |||||||||
Keywords | TRANSFERASE / glycoprotein / glycocyltransferase / HNK-1 epitope | |||||||||
Function / homology | Function and homology information galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / protein glycosylation / visual learning / carbohydrate metabolic process / Golgi membrane / intracellular membrane-bounded organelle ...galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / protein glycosylation / visual learning / carbohydrate metabolic process / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / extracellular region / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | |||||||||
Authors | Kakuda, S. / Shiba, T. / Ishiguro, M. / Tagawa, H. / Oka, S. / Kajihara, Y. / Kawasaki, T. / Wakatsuki, S. / Kato, R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Basis for Acceptor Substrate Recognition of a Human Glucuronyltransferase, GlcAT-P, an Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope HNK-1 Authors: Kakuda, S. / Shiba, T. / Ishiguro, M. / Tagawa, H. / Oka, S. / Kajihara, Y. / 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 | 1v84.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v84.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 1v84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v84_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1v84_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1v84_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 1v84_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/1v84 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/1v84 | HTTPS FTP |
-Related structure data
Related structure data | 1v82SC 1v83C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29038.408 Da / Num. of mol.: 2 / 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: Q9P2W7, galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine |
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#3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 365 molecules
#4: Chemical | #5: Chemical | ChemComp-TLA / | #6: Chemical | #7: 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: 2.61 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: PEG5000MME, di-sodium tartrate, 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: AR-NW12A / Wavelength: 0.974 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.974 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. all: 57144 / Num. obs: 57093 / % possible obs: 97.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.82→1.89 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.8 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V82 Resolution: 1.82→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.82→40 Å
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Refine LS restraints |
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