+Open data
-Basic information
Entry | Database: PDB / ID: 5fra | |||||||||
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Title | CBM40_CPF0721-6'SL | |||||||||
Components | SIALIDASE | |||||||||
Keywords | SUGAR BINDING PROTEIN / 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: 2 Å | |||||||||
Authors | Ribeiro, J.P. / 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 | 5fra.cif.gz | 254.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fra.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 5fra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fra_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 5fra_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5fra_validation.xml.gz | 50 KB | Display | |
Data in CIF | 5fra_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5fra ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5fra | HTTPS FTP |
-Related structure data
Related structure data | 5freC 2v73S C: citing same article (ref.) S: Starting model for refinement |
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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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4 |
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5 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 22402.824 Da / Num. of mol.: 6 / Fragment: CBM, UNP RESIDUES 48-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: NCTC 8237 / Plasmid: PNANI / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: A0A0H2YQR1 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 25% PEG 2K MME 0.3M CH3COONA 0.1M CH3COONA PH4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00185 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00185 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.69 Å / Num. obs: 74668 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V73 Resolution: 2→39.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.407 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. LOCAL NCS USED
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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: 28.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.69 Å
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Refine LS restraints |
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