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Yorodumi- PDB-1l2a: The Crystal Structure and Catalytic Mechanism of Cellobiohydrolas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l2a | |||||||||
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Title | The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome | |||||||||
Components | cellobiohydrolase | |||||||||
Keywords | HYDROLASE / alpha/alpha barrel | |||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (reducing end) / cellulose 1,4-beta-cellobiosidase activity (reducing end) / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Guimaraes, B.G. / Souchon, H. / Lytle, B.L. / Wu, J.H.D. / Alzari, P.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum Cellulosome. Authors: Guimaraes, B.G. / Souchon, H. / Lytle, B.L. / David Wu, J.H. / Alzari, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l2a.cif.gz | 769.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l2a.ent.gz | 642.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/1l2a ftp://data.pdbj.org/pub/pdb/validation_reports/l2/1l2a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 76638.320 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: cels / Plasmid: pTRXFUS / Production host: Escherichia coli (E. coli) References: UniProt: P38686, UniProt: P0C2S5*PLUS, cellulase #2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: ID14-3 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 223075 / Num. obs: 223075 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 90.5 |
Reflection | *PLUS Highest resolution: 2.5 Å / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 90.5 % / Rmerge(I) obs: 0.245 |
-Processing
Software |
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Refinement | Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.899 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.902 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.563 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor obs: 0.18312 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.247 / Rfactor Rwork: 0.209 |