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Yorodumi- PDB-5fkr: Unraveling the first step of xyloglucan degradation by the soil s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fkr | ||||||
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Title | Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase | ||||||
Components | ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, PUTATIVE, GLY74A | ||||||
Keywords | HYDROLASE / CELLVIBRIO JAPONICUS / XYLOGLUCAN SACCHARIFICATION / GLYCOSIDE HYDROLASE / CARBOHYDRATE BINDING MODULE / GREEN FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information xyloglucan metabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Attia, M. / Stepper, J. / Davies, G.J. / Brumer, H. | ||||||
Citation | Journal: FEBS J. / Year: 2016 Title: Functional and Structural Characterization of a Potent Gh74 Endo-Xyloglucanase from the Soil Saprophyte Cellvibrio Japonicus Unravels the First Step of Xyloglucan Degradation. Authors: Attia, M. / Stepper, J. / Davies, G.J. / Brumer, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fkr.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fkr.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fkr_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 5fkr_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 5fkr_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 5fkr_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/5fkr ftp://data.pdbj.org/pub/pdb/validation_reports/fk/5fkr | HTTPS FTP |
-Related structure data
Related structure data | 5fkqC 5fksC 5fktC 4lgnS 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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Unit cell |
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-Components
#1: Protein | Mass: 78284.070 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 35-765 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B3PKK9, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, xyloglucan-specific endo-beta-1,4-glucanase |
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#2: Chemical | ChemComp-BR / |
#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % / Description: NONE |
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Crystal grow | Details: 0.1 M TRIS (PH 7.8), 0.3 M POTASSIUM BROMIDE, 8 % PGA-LM |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→73.17 Å / Num. obs: 39506 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.28→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LGN Resolution: 2.28→73.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.602 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.243 / 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: 28.639 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→73.17 Å
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Refine LS restraints |
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