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Yorodumi- PDB-1g87: THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLUL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g87 | ||||||
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Title | THE CRYSTAL STRUCTURE OF ENDOGLUCANASE 9G FROM CLOSTRIDIUM CELLULOLYTICUM | ||||||
Components | ENDOCELLULASE 9G | ||||||
Keywords | HYDROLASE / ENDOGLUCANASE / CELLULASE 9G / CELLULOSE BINDING DOMAIN / (ALPHA/ALPHA)6-HELIX BARREL / BETA 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 1g87.cif.gz | 264.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g87.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g87_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 1g87_full_validation.pdf.gz | 470 KB | Display | |
Data in XML | 1g87_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 1g87_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g87 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g87 | HTTPS FTP |
-Related structure data
Related structure data | 1ga2C 1k72C 1kfgC 1js4S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 68061.086 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(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37700, cellulase |
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-Non-polymers , 5 types, 697 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-GOL / #6: 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 Å3/Da / Density % sol: 38.53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris, Mg Acetate, Isopropanol, Glycerol, pH 8.5, 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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI 111 OR 311 CHANNELS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 135088 / % possible obs: 97 % / Observed criterion σ(I): 1.7 / Redundancy: 2.1 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.371 / % possible all: 95.1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 95.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JS4 Resolution: 1.6→29.17 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.49 Å2 / ksol: 0.404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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