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- PDB-3vog: Catalytic domain of the cellobiohydrolase, CcCel6A, from Coprinop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vog | ||||||
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Title | Catalytic domain of the cellobiohydrolase, CcCel6A, from Coprinopsis cinerea | ||||||
![]() | Cellobiohydrolase | ||||||
![]() | HYDROLASE / Seven-stranded beta-alpha barrel / 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 | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 69.3 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 ![]() 3vohC ![]() 3voiC ![]() 3vojC ![]() 1bvwS 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 | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.24 % |
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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: Dec 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 61610 / % possible obs: 97.6 % / Redundancy: 9.97 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 41.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5.1 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BVW Resolution: 1.45→34.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.972 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / 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: 15.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.449→1.487 Å / Total num. of bins used: 20
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