+Open data
-Basic information
Entry | Database: PDB / ID: 1fo9 | ||||||
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Title | CRYSTAL STRUCTURE OF N-ACETYLGLUCOSAMINYLTRANSFERASE I | ||||||
Components | ALPHA-1,3-MANNOSYL-GLYCOPROTEIN BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / Apo Structure / 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 / protein N-linked glycosylation via asparagine / mannose metabolic process / 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 / protein N-linked glycosylation via asparagine / mannose metabolic process / 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: 1.5 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 | 1fo9.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fo9.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1fo9 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1fo9 | HTTPS FTP |
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-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: 40452.996 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT (RESIDUES 100-447) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: MODIFIED PVT-BAC-HIS / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P27115, alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase |
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#2: 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: 2.11 Å3/Da / Density % sol: 41.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG 8000, potassium chloride, glycerol, Tris, MES, UDP-GlcNAc, manganese chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.9914 |
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: 0.9914 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.24 Å / Num. all: 401605 / Num. obs: 99934 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.272 / Num. unique all: 31994 / % possible all: 77.8 |
Reflection | *PLUS Num. measured all: 401605 |
Reflection shell | *PLUS % possible obs: 77.8 % |
-Processing
Software |
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Refinement | Resolution: 1.5→38.24 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1599399.09 / 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: 46.51 Å2 / ksol: 0.3883 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→38.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / 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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