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Yorodumi- PDB-2am5: Crystal Structure of N-Acetylglucosaminyltransferase I in Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2am5 | ||||||
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Title | Crystal Structure of N-Acetylglucosaminyltransferase I in Complex with UDP | ||||||
Components | Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase | ||||||
Keywords | TRANSFERASE / N-Acetylglucosaminyltransferase / glycosyltransferase / UDP-GlcNAc / UDP | ||||||
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: 1.6 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 | 2am5.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2am5.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2am5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2am5_validation.pdf.gz | 812.2 KB | Display | wwPDB validaton report |
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Full document | 2am5_full_validation.pdf.gz | 813.4 KB | Display | |
Data in XML | 2am5_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2am5_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/2am5 ftp://data.pdbj.org/pub/pdb/validation_reports/am/2am5 | HTTPS FTP |
-Related structure data
Related structure data | 2am3C 2am4C 2apcC 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-UDP / | ||
#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: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 40% PEK 6000, 1M Tris, MnCl2, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Jul 11, 2003 |
Radiation | Monochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→31.94 Å / Num. all: 45466 / Num. obs: 44852 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 311496.49 / Observed criterion F min: 0.32 |
Reflection shell | Resolution: 1.6→1.7 Å / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FO9, 1FOA Resolution: 1.6→31.94 Å / Rfactor Rfree error: 0.004 / 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: 39.1505 Å2 / ksol: 0.416299 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.79 Å2 / Biso mean: 13.28 Å2 / Biso min: 2.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→31.94 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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