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Yorodumi- PDB-7s6n: N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s6n | ||||||
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Title | N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish | ||||||
Components | N-acetylglucosamine-1-phosphotransferase (GNPT) alpha (GNPTAB) catalytic domain,N-acetylglucosamine-1-phosphotransferase subunit beta | ||||||
Keywords | TRANSFERASE / GNPT / lysosome / mannose 6-phosphate / mucolipidosis | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / chondrocyte development / embryonic viscerocranium morphogenesis / carbohydrate phosphorylation / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization / bone development ...UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase / N-glycan processing to lysosome / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / chondrocyte development / embryonic viscerocranium morphogenesis / carbohydrate phosphorylation / embryonic cranial skeleton morphogenesis / cartilage development / lysosome organization / bone development / membrane => GO:0016020 / Golgi membrane / calcium ion binding / Golgi apparatus Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Gorelik, A. / Illes, K. / Nagar, B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structures of the mannose-6-phosphate pathway enzyme, GlcNAc-1-phosphotransferase. Authors: Gorelik, A. / Illes, K. / Bui, K.H. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s6n.cif.gz | 445 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s6n.ent.gz | 296.8 KB | Display | PDB format |
PDBx/mmJSON format | 7s6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/7s6n ftp://data.pdbj.org/pub/pdb/validation_reports/s6/7s6n | HTTPS FTP |
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-Related structure data
Related structure data | 7s69C 7sj2C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58363.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: gnptab, gnpta, si:ch211-234f20.3, zgc:122985 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5RGJ8 |
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-Sugars , 5 types, 9 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 380 molecules
#7: Chemical | #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: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG3350, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 63354 / % possible obs: 90.53 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.39 Å2 / Rrim(I) all: 0.115 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 4471 / CC1/2: 0.435 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold-2 Resolution: 2.7→48.42 Å / SU ML: 0.3011 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4454 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 46.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.42 Å
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Refine LS restraints |
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LS refinement shell |
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