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- PDB-7s69: N-acetylglucosamine-1-phosphotransferase (GNPT) gamma subunit (GN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7s69 | ||||||
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Title | N-acetylglucosamine-1-phosphotransferase (GNPT) gamma subunit (GNPTG), from clawed frog | ||||||
![]() | N-acetylglucosamine-1-phosphotransferase gamma subunit | ||||||
![]() | SUGAR BINDING PROTEIN / GNPT / mannose / mannose 6-phosphate receptor homology (MRH) domain / mucolipidosis | ||||||
Function / homology | ![]() N-acetylglucosamine-1-phosphotransferase subunit gamma / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / DMAP1-binding domain / DMAP1-binding domain profile. / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gorelik, A. / Illes, K. / Nagar, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.2 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s6nC ![]() 7sj2C ![]() 2lvxS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33412.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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 #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.1M bis-tris propane pH8, 0.2M KNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→50 Å / Num. obs: 8751 / % possible obs: 85 % / Redundancy: 8 % / Biso Wilson estimate: 58.1 Å2 / Rrim(I) all: 0.136 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 3.04→3.11 Å / Mean I/σ(I) obs: 1.29 / Num. unique obs: 577 / CC1/2: 0.812 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2LVX Resolution: 3.04→49.19 Å / SU ML: 0.3467 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0518 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: 56.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.04→49.19 Å
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Refine LS restraints |
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LS refinement shell |
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