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- PDB-7e9k: Crystal Structure of POMGNT2 in complex with UDP and mono-mannosy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e9k | |||||||||||||||
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Title | Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long peptide) | |||||||||||||||
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![]() | TRANSFERASE / Glycosyltransferase / O-mannose type glycosylation | |||||||||||||||
Function / homology | ![]() O-linked glycosylation / protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / protein O-linked mannosylation / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kuwabara, N. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan. Authors: Imae, R. / Kuwabara, N. / Manya, H. / Tanaka, T. / Tsuyuguchi, M. / Mizuno, M. / Endo, T. / Kato, R. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 571.9 KB | Display | ![]() |
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PDB format | ![]() | 374.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 83.4 KB | Display | |
Data in CIF | ![]() | 116.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 / Protein/peptide , 2 types, 6 molecules ABDECF
#1: Protein | Mass: 61563.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5NDF2, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase #2: Protein/peptide | Mass: 2317.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Sugars , 3 types, 15 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/MAN.gif)
#3: Polysaccharide | 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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#4: Sugar | ChemComp-NAG / #7: Sugar | |
-Non-polymers , 3 types, 914 molecules ![](data/chem/img/UDP.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-UDP / #6: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl (pH 8.0 or 8.5), 12-16% PEG 8000, 1% tacsimate (pH 7.0) PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→49.57 Å / Num. obs: 163077 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.05→2.09 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7958 / CC1/2: 0.761 / Rpim(I) all: 0.6 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: D_1300018733 Resolution: 2.05→49.55 Å / SU ML: 0.2494 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4566 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: 40.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→49.55 Å
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Refine LS restraints |
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LS refinement shell |
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