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Yorodumi- PDB-5zxg: Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zxg | ||||||
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Title | Cyclic alpha-maltosyl-(1-->6)-maltose hydrolase from Arthrobacter globiformis, ligand-free form | ||||||
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 / carbohydrate metabolic process / hydrolase activity / metal ion binding / Cyclic maltosyl-maltose hydrolase Function and homology information | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 5zxg.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zxg.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zxg_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 5zxg_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 5zxg_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 5zxg_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/5zxg ftp://data.pdbj.org/pub/pdb/validation_reports/zx/5zxg | HTTPS FTP |
-Related structure data
Related structure data | 6a0jC 6a0kC 6a0lC 1j0hS 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: Chemical | ChemComp-CA / | #3: 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: 2.44 Å3/Da / Density % sol: 49.57 % |
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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) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→89.9 Å / Num. obs: 35608 / % possible obs: 92.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 0.232 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 0.131 / CC1/2: 0.984 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J0H Resolution: 2.4→89.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.69 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.286 / 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: 26.543 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→89.9 Å
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Refine LS restraints |
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