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- PDB-2apc: Crystal Structure of N-Acetylglucosaminyltransferase I in Complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2apc | ||||||
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Title | Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP-GlcNAc phosphonate | ||||||
![]() | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | ||||||
![]() | TRANSFERASE / N-Acetylglucosaminyltransferase / glycosyltransferase / UDP-GlcNAc / UDP-GlcNAc phosphonate | ||||||
Function / homology | ![]() alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine catabolic process / protein N-acetylglucosaminyltransferase activity / mannose metabolic process / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Golgi medial cisterna / manganese ion binding / in utero embryonic development ...alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase / alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity / UDP-N-acetylglucosamine catabolic process / protein N-acetylglucosaminyltransferase activity / mannose metabolic process / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Golgi medial cisterna / manganese ion binding / in utero embryonic development / Golgi membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rini, J.M. / Gordon, R.D. | ||||||
![]() | ![]() Title: X-ray Crystal Structures of Rabbit N-acetylglucosaminyltransferase I (GnT I) in Complex with Donor Substrate Analogues. Authors: Gordon, R.D. / Sivarajah, P. / Satkunarajah, M. / Ma, D. / Tarling, C.A. / Vizitiu, D. / Withers, S.G. / Rini, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.6 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806.6 KB | Display | ![]() |
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Full document | ![]() | 808.3 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2am3C ![]() 2am4C ![]() 2am5C ![]() 1fo9S ![]() 1foaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 39725.172 Da / Num. of mol.: 1 / Fragment: residues 106-447 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P27115, alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-UDM / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 1 M Tris pH 7.9, 40% PEG 6000, MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2003 |
Radiation | Monochromator: SYCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9363 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43.51 Å / Num. all: 55630 / Num. obs: 54569 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.7 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 54 / Limit k min: 0 / Limit l max: 68 / Limit l min: 0 / Observed criterion F max: 194316.95 / Observed criterion F min: 0.32 |
Reflection shell | Resolution: 1.5→1.59 Å / % possible all: 86.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FOA, 1FO9 Resolution: 1.5→43.51 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 35.8371 Å2 / ksol: 0.379612 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.62 Å2 / Biso mean: 16.76 Å2 / Biso min: 5.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→43.51 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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