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Yorodumi- PDB-5ljf: Crystal structure of the endo-1,4-glucanase RBcel1 E135A with cel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ljf | ||||||||||||
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Title | Crystal structure of the endo-1,4-glucanase RBcel1 E135A with cellotriose | ||||||||||||
Components | EndoglucanaseCellulase | ||||||||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE FAMILY 5 / CELLULASE / TIM BARREL / BETA-1 / 4-ENDOGLUCANASE | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | uncultured bacterium (environmental samples) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73439601224 Å | ||||||||||||
Authors | Dutoit, R. / Collet, L. / Galleni, M. / Bauvois, C. | ||||||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Glycoside hydrolase family 5: structural snapshots highlighting the involvement of two conserved residues in catalysis. Authors: Collet, L. / Vander Wauven, C. / Oudjama, Y. / Galleni, M. / Dutoit, R. #1: Journal: ISME J / Year: 2009 Title: Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples. Authors: Berlemont, R. / Delsaute, M. / Pipers, D. / D'Amico, S. / Feller, G. / Galleni, M. / Power, P. #2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2013 Title: Three-dimensional structure of RBcel1, a metagenome-derived psychrotolerant family GH5 endoglucanase. Authors: Delsaute, M. / Berlemont, R. / Dehareng, D. / Van Elder, D. / Galleni, M. / Bauvois, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ljf.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ljf.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ljf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/5ljf ftp://data.pdbj.org/pub/pdb/validation_reports/lj/5ljf | HTTPS FTP |
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-Related structure data
Related structure data | 6zz3C 4ee9S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36324.016 Da / Num. of mol.: 2 / Mutation: E135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JI15, cellulase #2: Polysaccharide | #3: 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: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Crystals were grown at 19 C using the hanging drop method by mixing 2 uL of protein solution (385 uM of protein in 20 mM NaPi pH 6.5 and cellotriose 5 mM) , with 2 uL of resevoir buffer (100 ...Details: Crystals were grown at 19 C using the hanging drop method by mixing 2 uL of protein solution (385 uM of protein in 20 mM NaPi pH 6.5 and cellotriose 5 mM) , with 2 uL of resevoir buffer (100 mM Tris HCl pH 7.4 with 17.5 pc w/v polyethylene glycol 600) containing seeds. Crystals were cryoprotected by equilibrating 2 hours the drop against 500 uL reservoir containing 0.1M Tris PEG 600 30pc pH 7.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→47.09 Å / Num. obs: 70572 / % possible obs: 99 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.2870816768 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.81 |
Reflection shell | Resolution: 1.73→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.54 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EE9 polyalanine Resolution: 1.73439601224→38.918562621 Å / SU ML: 0.198744573079 / Cross valid method: FREE R-VALUE / σ(F): 1.35787498699 / Phase error: 21.8447173464
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3568679699 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73439601224→38.918562621 Å
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Refine LS restraints |
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LS refinement shell |
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