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Yorodumi- PDB-2vn6: The Clostridium cellulolyticum dockerin displays a dual binding m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vn6 | ||||||
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Title | The Clostridium cellulolyticum dockerin displays a dual binding mode for its cohesin partner | ||||||
Components |
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Keywords | CELL ADHESION / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / HYDROLASE / GLYCOSIDASE / CELLULOSE DEGRADATION | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM CELLULOLYTICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Pinheiro, B.A. / Prates, J.A.M. / Proctor, M.R. / Gilbert, H.J. / Davies, G.J. / Money, V.A. / Martinez-Fleites, C. / Bayer, E.A. / Fontes, C.M.G.A. / Fierobe, H.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Clostridium Cellulolyticum Dockerin Displays a Dual Binding Mode for its Cohesin Partner. Authors: Pinheiro, B.A. / Proctor, M.R. / Martinez-Fleites, C. / Prates, J.A.M. / Money, V.A. / Davies, G.J. / Bayer, E.A. / Fontes, C.M.G.A. / Fierobe, H.P. / Gilbert, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vn6.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vn6.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/2vn6 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/2vn6 | HTTPS FTP |
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-Related 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: 15557.599 Da / Num. of mol.: 1 / Fragment: RESIDUES 277-427 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q45996 | ||||
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#2: Protein | Mass: 7150.083 Da / Num. of mol.: 1 / Fragment: RESIDUES 410-473 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM CELLULOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17901 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 53.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→39.19 Å / Num. obs: 39149 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.49→1.57 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.49→19.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.693 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.073 / 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: 17.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→19.77 Å
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Refine LS restraints |
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