+Open data
-Basic information
Entry | Database: PDB / ID: 2vi0 | |||||||||
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Title | Lichenase CtLic26 in complex with a thio-oligosaccharide | |||||||||
Components | Endoglucanase H | |||||||||
Keywords | HYDROLASE / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / GLYCOSIDASE / CELLULOSE DEGRADATION / ENZYME GLYCOSIDE HYDROLASE LICHENASE BETA GLUCANASE GH26 G | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | |||||||||
Authors | Money, V.A. / Ducros, V.M. / Davies, G.J. | |||||||||
Citation | Journal: Org. Biomol. Chem. / Year: 2008 Title: Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants. Authors: Money, V.A. / Cartmell, A. / Guerreiro, C.I. / Ducros, V.M. / Fontes, C.M. / Gilbert, H.J. / Davies, G.J. #1: Journal: J.Biol.Chem. / Year: 2005 Title: How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides: Structure and Activity of a Clostridium Thermocellum Lichenase, Ctlic26A. Authors: Taylor, E.J. / Goyal, A. / Guerreiro, C.I.P.D. / Prates, J.A.M. / Money, V.A. / Ferry, N. / Morland, C. / Planas, A. / Macdonald, J.A. / Stick, R.V. / Gilbert, H.J. / Fontes, C.M.G.A. / Davies, G.J. #2: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006 Title: Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases. Authors: Money, V.A. / Smith, N.L. / Scaffidi, A. / Stick, R.V. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vi0.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vi0.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vi0 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vi0 | HTTPS FTP |
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-Related structure data
Related structure data | 2bv9S 2v80 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: 32045.432 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-304 / Mutation: G271E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: celH, Cthe_1472 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P16218, cellulase | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose | ||
#3: Polysaccharide | 4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside Source method: isolated from a genetically manipulated source | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDNonpolymer details | METHYL O-BETA-D-GLUCOPYRANOSYL- (1,4)-O-BETA-D-GLUCOPYRAN OSYL)- (1,3)-S-BETA-D-GLUCOPYRANOSYL- ( ...METHYL O-BETA-D-GLUCOPYRAN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.15 M AMMONIUM SULPHATE, 30 % PEG 5K, MME, 0.1 M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→34.88 Å / Num. obs: 3620 / % possible obs: 95.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.51→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BV9 Resolution: 1.51→34.88 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.274 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.081 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→34.88 Å
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