+Open data
-Basic information
Entry | Database: PDB / ID: 1fo8 | ||||||
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Title | CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINYLTRANSFERASE I | ||||||
Components | ALPHA-1,3-MANNOSYL-GLYCOPROTEIN BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / methylmercury derivative / ALPHA-1 / 3-MANNOSYL-GLYCOPROTEIN BETA-1 / 2-N-ACETYLGLUCOSAMINYLTRANSFERASE / N-ACETYLGLUCOSAMINYLTRANSFERASE I | ||||||
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 / Resolution: 1.4 Å | ||||||
Authors | Unligil, U.M. / Zhou, S. / Yuwaraj, S. / Sarkar, M. / Schachter, H. / Rini, J.M. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily. Authors: Unligil, U.M. / Zhou, S. / Yuwaraj, S. / Sarkar, M. / Schachter, H. / 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 | 1fo8.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fo8.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fo8_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 1fo8_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 1fo8_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1fo8_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1fo8 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1fo8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 39838.328 Da / Num. of mol.: 1 / Fragment: RESIDUES 105-447 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: MODIFIED PVT-BAC-HIS / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P27115, alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase |
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#2: Chemical | ChemComp-MMC / |
#3: 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: 2.14 Å3/Da / Density % sol: 42.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG 8000, POTASSIUM CHLORIDE, GLYCEROL, TRIS, MES, UDP-GLCNAC, MANGANESE CHLORIDE, METHYLMERCURY CHLORIDE, pH 7.90, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.0093 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→32.1 Å / Num. all: 348028 / Num. obs: 102233 / % possible obs: 78.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.227 / % possible all: 43.9 |
Reflection | *PLUS Num. measured all: 348028 |
Reflection shell | *PLUS % possible obs: 43.9 % |
-Processing
Software |
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Refinement | Resolution: 1.4→31.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1591251.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.54 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→31.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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