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Yorodumi- PDB-7jhl: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jhl | ||||||
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Title | Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP-N-acetylglucosamine | ||||||
Components | N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 | ||||||
Keywords | TRANSFERASE / glycosyltransferase / poly-N-acetyl-lactosamine | ||||||
Function / homology | Function and homology information N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor / axon guidance / sensory perception of smell / Golgi membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å | ||||||
Authors | Hao, Y. / Huang, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structures and mechanism of human glycosyltransferase beta 1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis. Authors: Hao, Y. / Crequer-Grandhomme, A. / Javier, N. / Singh, A. / Chen, H. / Manzanillo, P. / Lo, M.C. / Huang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jhl.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jhl.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jhl_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7jhl_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7jhl_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 7jhl_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/7jhl ftp://data.pdbj.org/pub/pdb/validation_reports/jh/7jhl | HTTPS FTP |
-Related structure data
Related structure data | 7jhiSC 7jhkC 7jhmC 7jhnC 7jhoC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43300.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B3GNT2, B3GALT7, B3GNT1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 5 types, 284 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 24% PEG1500, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 87 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.26→46.42 Å / Num. obs: 37963 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Net I/σ(I): 9.4 / Num. measured all: 255698 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JHI Resolution: 2.26→46.42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.44 Å2 / Biso mean: 39.0774 Å2 / Biso min: 14.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→46.42 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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