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- PDB-7yx8: Crystal structure of the AM0627 (E326A) inactive mutant in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yx8 | ||||||
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Title | Crystal structure of the AM0627 (E326A) inactive mutant in complex with PSGL-1-like bis-T glycopeptide and Zn2+ | ||||||
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![]() | HYDROLASE / Glycoprotease / mucinase / T antigen / Tn antigen / AM0627 | ||||||
Function / homology | M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Peptidase M60 domain-containing protein![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taleb, V. / Liao, Q. / Narimatsu, Y. / Garcia-Garcia, A. / Companon, I. / Borges, R.J. / Gonzalez-Ramirez, A.M. / Corzana, F. / Clausen, H. / Rovira, C. / Hurtado-Guerrero, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut. Authors: Taleb, V. / Liao, Q. / Narimatsu, Y. / Garcia-Garcia, A. / Companon, I. / Borges, R.J. / Gonzalez-Ramirez, A.M. / Corzana, F. / Clausen, H. / Rovira, C. / Hurtado-Guerrero, 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 | ![]() | 372.2 KB | Display | ![]() |
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PDB format | ![]() | 304.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 63.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein / Protein/peptide / Sugars , 3 types, 8 molecules ABFH
#1: Protein | Mass: 49951.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: This is the construct of the inactive mutant we used for crystallisation purposes. The five glycines in the N-terminus come from the vector. This is why the numbering is different for these glycines in the pdb. Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1012.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose |
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-Non-polymers , 3 types, 779 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
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#4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Monosaccharides, Buffer system 1 pH 6.5, Precipitant mix 2 (Molecular Dimensions) |
-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: Mar 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→172.61 Å / Num. obs: 167774 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 24256 / CC1/2: 0.624 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.684 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→86.3 Å
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Refine LS restraints |
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