+Open data
-Basic information
Entry | Database: PDB / ID: 1k72 | |||||||||
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Title | The X-ray Crystal Structure Of Cel9G Complexed With cellotriose | |||||||||
Components | Endoglucanase 9G | |||||||||
Keywords | HYDROLASE / endoglucanase / family 9 / cellotriose / cellulose binding domain / (alpha-alpha)6-barrel | |||||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Clostridium cellulolyticum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | |||||||||
Authors | Mandelman, D. / Belaich, A. / Belaich, J.P. / Aghajari, N. / Driguez, H. / Haser, R. | |||||||||
Citation | Journal: J.BACTERIOL. / Year: 2003 Title: X-Ray Crystal Structure of the Multidomain Endoglucanase Cel9G from Clostridium cellulolyticum Complexed with Natural and Synthetic Cello-Oligosaccharides Authors: Mandelman, D. / Belaich, A. / Belaich, J.P. / Aghajari, N. / Driguez, H. / Haser, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k72.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k72.ent.gz | 209.8 KB | Display | PDB format |
PDBx/mmJSON format | 1k72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k72_validation.pdf.gz | 471.4 KB | Display | wwPDB validaton report |
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Full document | 1k72_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 1k72_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 1k72_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k72 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k72 | HTTPS FTP |
-Related structure data
Related structure data | 1g87SC 1ga2C 1kfgC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 68107.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Gene: CelCCG / Plasmid: pET-22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P37700, cellulase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
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#3: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 775 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MG / #6: Chemical | #7: 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: 2.02 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Peg 4000, Hepes, MgAcO, Isopropanol, Glycerol, cellotriose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2001 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 98674 / Num. obs: 92853 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.3 / Redundancy: 4.4 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.8→1.82 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.314 / % possible all: 89.1 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 89.1 % / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1G87 Resolution: 1.8→36.31 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1357117.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.1973 Å2 / ksol: 0.364864 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→36.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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