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Yorodumi- PDB-8pn3: Crystal structure of the HC7-Glu200Ala mutant complexed to a tetr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pn3 | ||||||
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Title | Crystal structure of the HC7-Glu200Ala mutant complexed to a tetraglycopeptide. | ||||||
Components |
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Keywords | HYDROLASE / Mucinase / glycoprotease / cluster of O-glycans | ||||||
Function / homology | 2-acetamido-2-deoxy-alpha-D-galactopyranose Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Taleb, V. / Hurtado-Guerrero, R. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Catal / Year: 2024 Title: A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / ...Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / Joshi, H.J. / Hurtado-Guerrero, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pn3.cif.gz | 185.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pn3.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 8pn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pn3_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8pn3_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8pn3_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 8pn3_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pn3 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pn3 | HTTPS FTP |
-Related structure data
Related structure data | 8pmuC 8pn5C 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 12 molecules ABCD
#1: Protein | Mass: 74159.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: DN401_14795 / Production host: Escherichia coli (E. coli) #2: Protein/peptide | Mass: 1299.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Sugar | ChemComp-A2G / |
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-Non-polymers , 3 types, 845 molecules
#3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000 MES Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→20 Å / Num. obs: 140966 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.44→1.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 20377 / CC1/2: 0.646 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→19.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.229 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 16.001 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→19.9 Å
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