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- PDB-3abx: CcCel6C, a glycoside hydrolase family 6 enzyme, complexed with p-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3abx | |||||||||
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Title | CcCel6C, a glycoside hydrolase family 6 enzyme, complexed with p-nitrophenyl beta-D-cellotrioside | |||||||||
![]() | Cellobiohydrolase | |||||||||
![]() | HYDROLASE / seven-stranded beta-alpha barrel / cellulase / glycoside hydrolase family 6 / cellobiohydrolase | |||||||||
Function / homology | ![]() Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, Y. / Yoshida, M. / Kurakata, Y. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T. | |||||||||
![]() | ![]() Title: Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea Authors: Liu, Y. / Yoshida, M. / Kurakata, Y. / Miyazaki, T. / Igarashi, K. / Samejima, M. / Fukuda, K. / Nishikawa, A. / Tonozuka, T. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea Authors: Kurakata, Y. / Tonozuka, T. / Liu, Y. / Kaneko, S. / Nishikawa, A. / Fukuda, K. / Yoshida, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 74.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a64SC ![]() 3a9bC S: Starting model for refinement C: citing same article ( |
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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: 43631.105 Da / Num. of mol.: 1 / Fragment: UNP residues 20-403 Source method: isolated from a genetically manipulated source Details: described in Kurakata et al., Acta Cryst. Sect. F, 65, 140-143, 2009 Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B7X9Z2, cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 8000, 0.1M HEPES-KOH, 0.15M magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 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: 1.4→50 Å / Num. all: 63990 / Num. obs: 63990 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.3 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3A64 Resolution: 1.4→24.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / 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: 14.802 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.399→1.435 Å / Total num. of bins used: 20
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