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- PDB-5jjh: Crystal structure of amylomaltase from Corynebacterium glutamicum -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jjh | ||||||
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Title | Crystal structure of amylomaltase from Corynebacterium glutamicum | ||||||
![]() | 4-alpha-glucanotransferase | ||||||
![]() | TRANSFERASE / (beta/alpha)8-barrel | ||||||
Function / homology | Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / Glycoside hydrolase superfamily / carbohydrate metabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joo, S. / Kim, S. / Kim, K.-J. | ||||||
![]() | ![]() Title: Crystal structure of amylomaltase from Corynebacterium glutamicum Authors: Joo, S. / Seo, H. / Kim, S. / Kim, K.-J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 461.7 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 49.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4s3pS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: A0A0R7P4S4, UniProt: Q8NNA7*PLUS, 4-alpha-glucanotransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 % |
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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: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 18, 2016 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 71588 / % possible obs: 98.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.8→1.83 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4S3P Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.212 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.12 / 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: 102.2 Å2 / Biso mean: 27.346 Å2 / Biso min: 11.48 Å2
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Refinement step | Cycle: final / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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