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Yorodumi- PDB-2apc: Crystal Structure of N-Acetylglucosaminyltransferase I in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2apc | ||||||
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Title | Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP-GlcNAc phosphonate | ||||||
Components | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | ||||||
Keywords | TRANSFERASE / N-Acetylglucosaminyltransferase / glycosyltransferase / UDP-GlcNAc / UDP-GlcNAc phosphonate | ||||||
Function / homology | Function and homology information 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 | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Rini, J.M. / Gordon, R.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2apc.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2apc.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 2apc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2apc_validation.pdf.gz | 806.6 KB | Display | wwPDB validaton report |
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Full document | 2apc_full_validation.pdf.gz | 808.3 KB | Display | |
Data in XML | 2apc_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 2apc_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/2apc ftp://data.pdbj.org/pub/pdb/validation_reports/ap/2apc | HTTPS FTP |
-Related structure data
Related structure data | 2am3C 2am4C 2am5C 1fo9S 1foaS 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
#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.) Oryctolagus cuniculus (rabbit) / Cell line: GnT1-5G5 / Production host: Cricetulus griseus (Chinese hamster) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9363 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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