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- PDB-3voi: CcCel6A catalytic domain complexed with p-nitrophenyl beta-D-cell... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3voi | ||||||
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Title | CcCel6A catalytic domain complexed with p-nitrophenyl beta-D-cellotrioside | ||||||
![]() | Cellobiohydrolase | ||||||
![]() | HYDROLASE / Seven-stranded beta-alpha barrel / Glycoside hydrolase family 6 / Cellobiohydrolase | ||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tamura, M. / Miyazaki, T. / Tanaka, Y. / Yoshida, M. / Nishikawa, A. / Tonozuka, T. | ||||||
![]() | ![]() Title: Comparison of the structural changes in two cellobiohydrolases, CcCel6A and CcCel6C, from Coprinopsis cinerea - a tweezer-like motion in the structure of CcCel6C Authors: Tamura, M. / Miyazaki, T. / Tanaka, Y. / Yoshida, M. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.5 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vofC ![]() 3vogC ![]() 3vohSC ![]() 3vojC 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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Unit cell |
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Components
#1: Protein | Mass: 41049.859 Da / Num. of mol.: 1 / Fragment: UNP residues 93-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B7X9Z0, cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||
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#2: Chemical | #3: Chemical | ChemComp-RCB / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 8000, 0.1M HEPES-KOH, 0.1M magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22349 / % possible obs: 95.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 8.3 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VOH Resolution: 2→30.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.2 / 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: 17.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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