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Yorodumi- PDB-5fu3: The complexity of the Ruminococcus flavefaciens cellulosome refle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fu3 | |||||||||
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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 | beta-cellotriose / Carbohydrate binding module Function and homology information | |||||||||
Biological species | RUMINOCOCCUS FLAVEFACIENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||
Authors | Basle, A. / Luis, A.S. / Venditto, I. / Gilbert, H.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / 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.R. / Dourado, C.G. / Ferreira, L.M.A. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G.T. / Fontes, C.M.G.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fu3.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fu3.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5fu3 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5fu3 | HTTPS FTP |
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-Related structure data
Related structure data | 4d3lC 4v17C 4v18C 4v1bC 4v1iC 4v1kC 4v1lC 5aosC 5aotSC 5fu2C 5fu4C 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: 11834.903 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: A0A1A9TAF4*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-NA / | #4: 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: 2.03 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | Details: 20 MM NA FORMATE 20MM NH4 ACETATE 20 MM NA3 CITRATE 20 MM NAK TARTRATE (RACEMIC) 20 MM NA OXAMATE 50 MM IMIDAZOLE 50 MM MES PH 6.5 12.5% MPD 12.5% PEG 1000 12.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97959 |
Detector | Date: Sep 20, 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: 1.61→43.84 Å / Num. obs: 24439 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5AOT Resolution: 1.61→43.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.85 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC BFACTOR
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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: 20.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→43.84 Å
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Refine LS restraints |
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