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Yorodumi- PDB-2d7r: Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d7r | ||||||||||||
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Title | Crystal structure of pp-GalNAc-T10 complexed with GalNAc-Ser on lectin domain | ||||||||||||
Components | Polypeptide N-acetylgalactosaminyltransferase 10 | ||||||||||||
Keywords | TRANSFERASE / beta trefoil / Rossmann fold | ||||||||||||
Function / homology | Function and homology information polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / Golgi membrane / Golgi apparatus / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Kubota, T. / Shiba, T. / Sugioka, S. / Kato, R. / Wakatsuki, S. / Narimatsu, H. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural basis of carbohydrate transfer activity by human UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase (pp-GalNAc-T10) Authors: Kubota, T. / Shiba, T. / Sugioka, S. / Furukawa, S. / Sawaki, H. / Kato, R. / Wakatsuki, S. / Narimatsu, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d7r.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d7r.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/2d7r ftp://data.pdbj.org/pub/pdb/validation_reports/d7/2d7r | HTTPS FTP |
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-Related structure data
Related structure data | 2d7iSC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65472.305 Da / Num. of mol.: 1 / Fragment: residues 40-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 References: UniProt: Q86SR1, polypeptide N-acetylgalactosaminyltransferase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Sugar | #4: Sugar | ChemComp-NGA / | #8: Sugar | ChemComp-A2G / | |
-Non-polymers , 4 types, 77 molecules
#5: Chemical | ChemComp-MN / |
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#6: Chemical | ChemComp-UDP / |
#7: Chemical | ChemComp-SER / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 4% PEG 3350, 0.05M sodium thiocyanate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 19156 / Num. obs: 18964 / % possible obs: 99 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.494 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID: 2D7I Resolution: 2.8→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
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Refine LS restraints |
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