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Yorodumi- PDB-1edg: SINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1edg | ||||||
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Title | SINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF CELCCA CARRIED OUT AT 15 DEGREE C | ||||||
Components | ENDOGLUCANASE A | ||||||
Keywords | CELLULOSE DEGRADATION / FAMILY A / CELLULASES / XYLANASES / FAMILY 5 OF GLYCOSYL HYDROLASE | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium cellulolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Ducros, V. / Czjzek, M. / Haser, R. | ||||||
Citation | Journal: Structure / Year: 1995 Title: Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5. Authors: Ducros, V. / Czjzek, M. / Belaich, A. / Gaudin, C. / Fierobe, H.P. / Belaich, J.P. / Davies, G.J. / Haser, R. #1: Journal: J.Bacteriol. / Year: 1991 Title: Characterization of Endoglucanase a from Clostridium Cellulolyticum Authors: Fierobe, H.P. / Gaudin, C. / Belaich, A. / Loutfi, M. / Faure, E. / Bagnara, C. / Baty, D. / Belaich, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1edg.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1edg.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1edg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1edg_validation.pdf.gz | 410.9 KB | Display | wwPDB validaton report |
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Full document | 1edg_full_validation.pdf.gz | 413.6 KB | Display | |
Data in XML | 1edg_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1edg_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1edg ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1edg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43135.414 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, C TERMINUS TRUNCATED Source method: isolated from a genetically manipulated source Details: FAMILY 5 OF GLYCOSYL HYDROLASES / Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Strain: H10 / Gene: CELCCA / Plasmid: PJF118EH / Gene (production host): CELCCA / Production host: Escherichia coli (E. coli) / References: UniProt: P17901, cellulase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6 Details: CRYSTALS WERE GROWN AT 4 DEGREES C AND PH 6.0, temperature 277K | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Roig, V., (1993) J. Mol. Biol., 233, 325. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.6→20 Å / Num. obs: 59967 / % possible obs: 98 % / Observed criterion σ(I): 2.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 | |||||||||||||||
Reflection | *PLUS Highest resolution: 1.6 Å / Num. measured all: 355167 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Resolution: 1.6→7 Å / σ(F): 2 Details: THE SIDE CHAIN ATOMS OF TRP 181 AND ARG 358 WERE MODELED WITH PARTIAL OCCUPATION OF 0.7. THE SIDE CHAIN ATOMS OF ASN 46 WERE MODELED WITH PARTIAL OCCUPATION OF 0.6.
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Displacement parameters | Biso mean: 17.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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