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- PDB-5b6t: Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b6t | ||||||
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Title | Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase complexed with Pb | ||||||
![]() | Glycosyl hydrolase family 62 protein | ||||||
![]() | HYDROLASE / Coprinopsis cinerea / alpha-L-arabinofuranosidase / arabinoxylan / GH62 / hemicellulose | ||||||
Function / homology | ![]() L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cellulose binding / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tonozuka, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Catalytic Domain of alpha-L-Arabinofuranosidase from Coprinopsis cinerea, CcAbf62A, Provides Insights into Structure-Function Relationships in Glycoside Hydrolase Family 62 Authors: Tonozuka, T. / Tanaka, Y. / Okuyama, S. / Miyazaki, T. / Nishikawa, A. / 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 | ![]() | 153.5 KB | Display | ![]() |
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PDB format | ![]() | 117.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 46 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b6sC ![]() 4n4bS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36640.316 Da / Num. of mol.: 2 / Fragment: UNP residues 82-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_01577 / Plasmid: pET21a / Production host: ![]() ![]() References: UniProt: A8NI40, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | ChemComp-PB / | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES buffer, NaBr, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95064 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→27.63 Å / Num. obs: 321802 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4N4B Resolution: 1.48→27.63 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.281 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.522 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→27.63 Å
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Refine LS restraints |
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