+Open data
-Basic information
Entry | Database: PDB / ID: 5fre | |||||||||
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Title | Characterization of a novel CBM from Clostridium perfringens | |||||||||
Components | EXO-ALPHA-SIALIDASE | |||||||||
Keywords | HYDROLASE / CBM40 | |||||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | CLOSTRIDIUM PERFRINGENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Ribeiro, J. / Pau, W. / Pifferi, C. / Renaudet, O. / Varrot, A. / Mahal, L.K. / Imberty, A. | |||||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Characterization of a High-Affinity Sialic Acid-Specific Cbm40 from Clostridium Perfringens and Engineering of a Divalent Form. Authors: Ribeiro, J.P. / Pau, W. / Pifferi, C. / Renaudet, O. / Varrot, A. / Mahal, L.K. / Imberty, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fre.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fre.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fre_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5fre_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5fre_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 5fre_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5fre ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5fre | HTTPS FTP |
-Related structure data
Related structure data | 5fraSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 22103.541 Da / Num. of mol.: 3 / Fragment: CBM Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC 8237 / Plasmid: PNANI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2YQR1 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 524 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | PART OF THE SIALIDASE NANI SEQUENCE |
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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: 2.47 Å3/Da / Density % sol: 50.3 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 0.1M CH3COONA PH 4.5, 0.2M (CH3CHOO)2CA, 8% (PEG 550 MME AND PEG 20,000) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979761 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979761 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.69 Å / Num. obs: 50882 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FRA Resolution: 1.9→40.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.207 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 18.228 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.61 Å
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