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- PDB-2wob: 3b' carbohydrate-binding module from the Cel9V glycoside hydrolas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wob | ||||||
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Title | 3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum. Orthorhombic structure | ||||||
![]() | GLYCOSIDE HYDROLASE, FAMILY 9 | ||||||
![]() | HYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE | ||||||
Function / homology | ![]() cellulose binding / cellulase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Petkun, S. / Jindou, S. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 83.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.5 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wnxC ![]() 2wo4C ![]() 2w04S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18649.406 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE-BINDING MODULE 3B', RESIDUES 731-888 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.21 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.2 M AMMONIUM ACETATE, 0.1 M TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 30% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 8, 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: 2→50 Å / Num. obs: 41368 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 89.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W04 Resolution: 2→121.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.595 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY ACCORDING TO HIGHER RESOLUTION STRUCTURE 2WNX.
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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: 33.402 Å2
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Refinement step | Cycle: LAST / Resolution: 2→121.18 Å
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Refine LS restraints |
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