[English] 日本語
Yorodumi- PDB-5b6s: Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b6s | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase | ||||||
Components | Glycosyl hydrolase family 62 protein | ||||||
Keywords | HYDROLASE / Coprinopsis cinerea / alpha-L-arabinofuranosidase / arabinoxylan / GH62 / hemicellulose | ||||||
Function / homology | Function and homology information 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 | Coprinopsis cinerea (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tonozuka, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Appl. Biochem. Biotechnol. / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5b6s.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5b6s.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 5b6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b6s ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b6s | HTTPS FTP |
---|
-Related structure data
Related structure data | 5b6tSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (fungus) Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_01577 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) References: UniProt: A8NI40, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.41 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES buffer, NaBr, PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→74.1 Å / Num. obs: 59017 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.7 / % possible all: 97.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B6T Resolution: 1.7→74.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.261 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→74.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|