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- PDB-8h1n: Crystal structure of glucose-2-epimerase mutant_D254A in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h1n | ||||||||||||||||||
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Title | Crystal structure of glucose-2-epimerase mutant_D254A in complex with D-Glucitol from Runella slithyformis Runsl_4512 | ||||||||||||||||||
![]() | N-acylglucosamine 2-epimerase | ||||||||||||||||||
![]() | ISOMERASE / mutant form / complex / Runsl | ||||||||||||||||||
Function / homology | ![]() N-acylglucosamine 2-epimerase activity / sulfoquinovose isomerase activity / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / carbohydrate metabolic process Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Wang, H. / Sun, X.M. / Saburi, W. / Yu, J. / Yao, M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis. Authors: Wang, H. / Sun, X. / Saburi, W. / Hashiguchi, S. / Yu, J. / Ose, T. / Mori, H. / Yao, M. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.7 KB | Display | ![]() |
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Full document | ![]() | 721.1 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h1kC ![]() 8h1lC ![]() 8h1mC ![]() 3vw5S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49039.062 Da / Num. of mol.: 1 / Mutation: D254A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Sugar | ChemComp-SOR / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.83 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 3.6M sodium formate, 486 mM D-glucitol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→46.08 Å / Num. obs: 20958 / % possible obs: 99.69 % / Redundancy: 25.9 % / Biso Wilson estimate: 35.21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.69 / Net I/σ(I): 8.68 |
Reflection shell | Resolution: 2.67→2.77 Å / Num. unique obs: 1995 / CC1/2: 0.675 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3vw5 Resolution: 2.67→46.08 Å / SU ML: 0.335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5066 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→46.08 Å
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Refine LS restraints |
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LS refinement shell |
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