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- PDB-4m24: Crystal structure of the endo-1,4-glucanase, RBcel1, in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m24 | |||||||||
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Title | Crystal structure of the endo-1,4-glucanase, RBcel1, in complex with cellobiose | |||||||||
![]() | Endoglucanase | |||||||||
![]() | HYDROLASE / GLYCOSYL HYDROLASE FAMILY 5 / CELLULASE / TIM BARREL / BETA-1 / 4-ENDOGLUCANASE | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Delsaute, M. / Berlemont, R. / Van elder, D. / Galleni, M. / Bauvois, C. | |||||||||
![]() | ![]() Title: Characterisation of two GH family 5 cellulases required for bacterial cellulose production Authors: Delsaute, M. / Bauvois, C. / Wei, Q. / Dehareng, D. / Byttebier, V. / Van elder, D. / Paquot, M. / Cornelis, P. / Galleni, M. / Berlemont, 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.4 KB | Display | ![]() |
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PDB format | ![]() | 135.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gzjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36382.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET-22b:RBcel1 / Production host: ![]() ![]() | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.44 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: RBCel1 in 20 mM NaPi pH 6.5 and cellobiose 1% , was mixed 2:2 with well buffer (100mM Tris HCl pH 6.0 with 20 % w/v polyethylene glycol 600) using the hanging drop method with 500mL well ...Details: RBCel1 in 20 mM NaPi pH 6.5 and cellobiose 1% , was mixed 2:2 with well buffer (100mM Tris HCl pH 6.0 with 20 % w/v polyethylene glycol 600) using the hanging drop method with 500mL well buffer in the well of the crystallization tray, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979718 Å / Relative weight: 1 |
Reflection | Resolution: 1.386→49.26 Å / Num. all: 66287 / Num. obs: 64593 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 9.82 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.39→1.44 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6112 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GZJ Resolution: 1.386→30.112 Å / SU ML: 0.1 / σ(F): 2 / Phase error: 14.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.386→30.112 Å
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Refine LS restraints |
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LS refinement shell |
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