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Yorodumi- PDB-1ut9: Structural Basis for the Exocellulase Activity of the Cellobiohyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ut9 | ||||||
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Title | Structural Basis for the Exocellulase Activity of the Cellobiohydrolase CbhA from C. thermocellum | ||||||
Components | CELLULOSE 1,4-BETA-CELLOBIOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 9 / CELLOBIOHYDROLASE | ||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase activity / cellulase / cellulase activity / cellulose catabolic process Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.1 Å | ||||||
Authors | Schubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum. Authors: Schubot, F.D. / Kataeva, I.A. / Chang, J. / Shah, A.K. / Ljungdahl, L.G. / Rose, J.P. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ut9.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ut9.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ut9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ut9_validation.pdf.gz | 418.3 KB | Display | wwPDB validaton report |
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Full document | 1ut9_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 1ut9_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 1ut9_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1ut9 ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1ut9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68608.016 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 208-816 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Plasmid: PET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6RSN8*PLUS, cellulase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: batch mode / pH: 8.5 / Details: 20% PEG4000, 0.2M (NH4)2SO4, 0.1M TRIS, PH 7.0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 273 K / pH: 8.5 / Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: RIGAKU HI RES OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→69 Å / Num. obs: 41182 / % possible obs: 92 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 66 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 69 Å / % possible obs: 91.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 65.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.1→69.01 Å / SU B: 3.621 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PLEASE NOTE THAT THIS ENTRY CONTAINS ATOMS REFINED WITH 0.00 OCCUPANCY.
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Displacement parameters | Biso mean: 17.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→69.01 Å
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 69 Å / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.147 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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