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Yorodumi- PDB-2bod: Catalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fu... -
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-Basic information
Entry | Database: PDB / ID: 2bod | |||||||||
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Title | Catalytic domain of endo-1,4-glucanase Cel6A from Thermobifida fusca in complex with methyl cellobiosyl-4-thio-beta-cellobioside | |||||||||
Components | ENDOGLUCANASE E-2 | |||||||||
Keywords | HYDROLASE / ENDOGLUCANASE / THERMOBIFIDA FUSCA / TIM A/B FOLD / GLYCOSIDE HYDROLASE FAMILY 6 / METHYL CELLOBIOSYL-4-THIO-BETA-CELLOBIOSIDE / CARBOHYDRATE METABOLISM / CELLULOSE DEGRADATION / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION | |||||||||
Function / homology | Function and homology information cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | THERMOMONOSPORA FUSCA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Larsson, A.M. / Bergfors, T. / Dultz, E. / Irwin, D.C. / Roos, A. / Driguez, H. / Wilson, D.B. / Jones, T.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structure of Thermobifida Fusca Endoglucanase Cel6A in Complex with Substrate and Inhibitor: The Role of Tyrosine Y73 in Substrate Ring Distortion. Authors: Larsson, A.M. / Bergfors, T. / Dultz, E. / Irwin, D.C. / Roos, A. / Driguez, H. / Wilson, D.B. / Jones, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bod.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bod.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2bod ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2bod | HTTPS FTP |
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-Related structure data
Related structure data | 2boeC 2bofC 2bogC 1tmlS 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
#1: Protein | Mass: 30436.793 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOMONOSPORA FUSCA (bacteria) / Plasmid: POS12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26222, cellulase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Compound details | ENDOHYDROL |
-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: 36.7 % |
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Crystal grow | Details: 20-30% POLYETHYLENGLYCOL 4000 AND 0.15-0.34 M SODIUM MALONATE, PH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.134 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 2002 / Details: SI MIRROR COATED WITH PLATINUM |
Radiation | Monochromator: ASYMMETRICALLY CUT SINGLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.134 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→18.4 Å / Num. obs: 38138 / % possible obs: 99.3 % / Observed criterion σ(I): 6 / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.115 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.263 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TML Resolution: 1.5→18.38 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.508 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 14.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.38 Å
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Refine LS restraints |
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