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Yorodumi- PDB-6a0k: Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a0k | |||||||||
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Title | Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter globiformis, complex with panose | |||||||||
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: 1.94 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a0k.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a0k.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a0k ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a0k | HTTPS FTP |
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-Related structure data
Related structure data | 5zxgC 6a0jC 6a0lC 5xzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51664.258 Da / Num. of mol.: 2 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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium citrate, 0.22 M Ammonium sulfate, 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→90.1 Å / Num. obs: 72961 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 0.137 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 0.024 / Num. unique obs: 69198 / CC1/2: 0.791 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XZG Resolution: 1.94→90.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.921 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.505 Å2
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Refinement step | Cycle: 1 / Resolution: 1.94→90.1 Å
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Refine LS restraints |
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