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- PDB-8yud: Crystal structure of Xylose isomerase from Streptomyces avermitilis -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yud | ||||||
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Title | Crystal structure of Xylose isomerase from Streptomyces avermitilis | ||||||
![]() | Xylose isomerase | ||||||
![]() | ISOMERASE / Xylose isomerase / glucose isomerase / Streptomyces avermitilis | ||||||
Function / homology | ![]() xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nam, K.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Xylose isomerase from Streptomyces avermitilis Authors: Nam, K.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 436.9 KB | Display | ![]() |
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PDB format | ![]() | 360.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.8 MB | Display | ![]() |
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Full document | ![]() | 5.7 MB | Display | |
Data in XML | ![]() | 75.5 KB | Display | |
Data in CIF | ![]() | 103.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 42886.043 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: Tris, Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 54119 / % possible obs: 97.8 % / Redundancy: 6.4 % / CC1/2: 0.977 / Net I/σ(I): 11.24 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 2664 / CC1/2: 0.627 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→34.21 Å
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Refine LS restraints |
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LS refinement shell |
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