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Yorodumi- PDB-5fu4: The complexity of the Ruminococcus flavefaciens cellulosome refle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fu4 | |||||||||
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Title | The complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition | |||||||||
Components | CBM74-RFGH5 | |||||||||
Keywords | SUGAR BINDING PROTEIN / CELLULOSOME / CARBOHYDRATE BINDING MODULE / RUMINOCCOCUS FLAVEFACIENS / ENDOGLUCANASE CEL5A | |||||||||
Function / homology | Cbm74-rfgh5 Function and homology information | |||||||||
Biological species | RUMINOCOCCUS FLAVEFACIENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Basle, A. / Luis, A.S. / Venditto, I. / Gilbert, H.J. | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition. Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / ...Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M. / Dourado, C.G. / Ferreira, L.M. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G. / Fontes, C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fu4.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fu4.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fu4_validation.pdf.gz | 961.5 KB | Display | wwPDB validaton report |
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Full document | 5fu4_full_validation.pdf.gz | 961.7 KB | Display | |
Data in XML | 5fu4_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5fu4_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fu4 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fu4 | HTTPS FTP |
-Related structure data
Related structure data | 4d3lC 4v17C 4v18C 4v1bC 4v1iC 4v1kC 4v1lC 5aosC 5aotSC 5fu2C 5fu3C 5fu5C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11719.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1A9TA80*PLUS #2: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Sequence details | W490A MUTANT | |
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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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Details: 25% W/V PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97959 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.32 Å / Num. obs: 13038 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AOT Resolution: 2→40.32 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.802 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. W490A MUTANT
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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: 28.427 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.32 Å
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Refine LS restraints |
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