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Yorodumi- PDB-2wo4: 3b' carbohydrate-binding module from the Cel9V glycoside hydrolas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wo4 | ||||||
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Title | 3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum, in-house data | ||||||
Components | GLYCOSIDE HYDROLASE, FAMILY 9 | ||||||
Keywords | HYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE | ||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Petkun, S. / Jindou, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structure of a Family 3B' Carbohydrate-Binding Module from the Cel9V Glycoside Hydrolase from Clostridium Thermocellum: Structural Diversity and Implications for Carbohydrate Binding Authors: Petkun, S. / Jindou, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F. #1: Journal: Fems Microbiol.Lett. / Year: 2006 Title: Novel Architecture of Family-9 Glycoside Hydrolases Identified in Cellulosomal Enzymes of Acetivibrio Cellulolyticus and Clostridium Thermocellum. Authors: Jindou, S. / Xu, Q. / Kenig, R. / Shulman, M. / Shoham, Y. / Bayer, E.A. / Lamed, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wo4.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wo4.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wo4 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wo4 | HTTPS FTP |
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-Related structure data
Related structure data | 2wnxC 2wobC 1nbcS C: citing same article (ref.) S: Starting model for refinement |
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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: 18649.406 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE-BINDING MODULE3B', RESIDUES 731-888 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DJ30 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.9 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 1.8 M AMMONIUM SULFATE, 0.1 M CITRIC ACID PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Date: May 5, 2004 / Details: OSMIC CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30 Å / Num. obs: 23006 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 32.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NBC Resolution: 1.85→55.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.206 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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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: 26.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→55.98 Å
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Refine LS restraints |
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