[English] 日本語
Yorodumi- PDB-6a0j: Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a0j | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter globiformis, complex with Cyclic alpha-maltosyl-(1-->6)-maltose | |||||||||
Components | Cyclic maltosyl-maltose hydrolase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily / hydrolase activity / carbohydrate metabolic process / Cyclic maltosyl-maltose hydrolase Function and homology information | |||||||||
Biological species | Arthrobacter globiformis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Kohno, M. / Arakawa, T. / Mori, T. / Nishimoto, T. / Fushinobu, S. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural features of a bacterial cyclic alpha-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis. Authors: Kohno, M. / Arakawa, T. / Ota, H. / Mori, T. / Nishimoto, T. / Fushinobu, S. #1: Journal: Biosci. Biotechnol. Biochem. / Year: 2008 Title: Purification and characterization of cyclic maltosyl-(1-->6)-maltose hydrolase and alpha-glucosidase from an Arthrobacter globiformis strain. Authors: Mori, T. / Nishimoto, T. / Okura, T. / Chaen, H. / Fukuda, S. #2: Journal: Journal of Applied Glycoscience / Year: 2011 Title: Cloning, Sequencing and Expression of the Genes Encoding Cyclic alpha-Maltosyl-(1-->6)-maltose Hydrolase and alpha-Glucosidase from an Arthrobacter globiformis Strain Authors: Mori, T. / Nishimoto, T. / Okura, T. / Chaen, H. / Fukuda, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6a0j.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6a0j.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0j ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0j | HTTPS FTP |
---|
-Related structure data
Related structure data | 5zxgC 6a0kC 6a0lC 5xzgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 51663.270 Da / Num. of mol.: 1 / Mutation: D201N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: cmmF / Production host: Escherichia coli (E. coli) / References: UniProt: D2YYE1 |
---|---|
#2: Polysaccharide | Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.3 Details: 0.1 M Glycine-NaOH, 0.2 M Lithium sulfate, 0.8 M Sodium/potassium tartrate, 5 mM Cyclic alpha-maltosyl-(1-->6)-maltose |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→68.7 Å / Num. obs: 73605 / % possible obs: 98.2 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 0.295 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 0.06 / Num. unique obs: 69714 / CC1/2: 0.959 / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XZG Resolution: 1.6→68.67 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.292 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / 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: 17.143 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→68.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|