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Yorodumi- PDB-6xfi: Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xfi | ||||||
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Title | Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2): Structural Basis for Inherited Muscular Dystrophies | ||||||
Components | Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 | ||||||
Keywords | TRANSFERASE / muscular dystrophy / alpha-dystroglycan / O-mannosylation / POMGNT2 | ||||||
Function / homology | Function and homology information protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / O-linked glycosylation / protein O-linked mannosylation / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / glycosyltransferase activity / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Halmo, S.M. / Yeh, J. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies. Authors: Yang, J.Y. / Halmo, S.M. / Praissman, J. / Chapla, D. / Singh, D. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xfi.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xfi.ent.gz | 97.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/6xfi ftp://data.pdbj.org/pub/pdb/validation_reports/xf/6xfi | 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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-Components
#1: Protein | Mass: 61062.449 Da / Num. of mol.: 1 / Fragment: UNP residues 52-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase | ||||
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#2: Chemical | ChemComp-UDP / | ||||
#3: Sugar | ChemComp-NAG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.1 M potassium/sodium tartrate, 0.1 M Bis-Tris, pH 7.5, 10% PEG10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 49420 / % possible obs: 99.7 % / Redundancy: 11.3 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.97→2.08 Å / Num. unique obs: 4759 / CC1/2: 0.298 / CC star: 0.678 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→40 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.74 / 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: 107.17 Å2 / Biso mean: 40.1046 Å2 / Biso min: 16.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→40 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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