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Yorodumi- PDB-5b68: Crystal structure of apo amylomaltase from Corynebacterium glutamicum -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b68 | ||||||
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Title | Crystal structure of apo amylomaltase from Corynebacterium glutamicum | ||||||
Components | 4-alpha-glucanotransferase | ||||||
Keywords | TRANSFERASE / (beta/alpha)8-barrel | ||||||
Function / homology | Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase Function and homology information | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Joo, S. / Kim, S. / Kim, K.-J. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2016 Title: Crystal Structure of Amylomaltase from Corynebacterium glutamicum. Authors: Joo, S. / Kim, S. / Seo, H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b68.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b68.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 5b68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b68_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 5b68_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 5b68_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 5b68_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b68 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b68 | HTTPS FTP |
-Related structure data
Related structure data | 5jjhS S: Starting model for refinement |
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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: 79676.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A0R7P4S4, UniProt: Q8NNA7*PLUS, 4-alpha-glucanotransferase | ||||
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#2: Chemical | ChemComp-BTB / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate, Bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 2, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 81053 / % possible obs: 96.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.068 / Net I/av σ(I): 34.725 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JJH Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.671 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.107 / 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 max: 109.2 Å2 / Biso mean: 30.509 Å2 / Biso min: 14.87 Å2
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Refinement step | Cycle: final / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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