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Yorodumi- PDB-8h1n: Crystal structure of glucose-2-epimerase mutant_D254A in complex ... -
+Open data
-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 | ||||||||||||||||||
Components | N-acylglucosamine 2-epimerase | ||||||||||||||||||
Keywords | ISOMERASE / mutant form / complex / Runsl | ||||||||||||||||||
Function / homology | N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / isomerase activity / carbohydrate metabolic process / FORMIC ACID / sorbitol / N-acylglucosamine 2-epimerase Function and homology information | ||||||||||||||||||
Biological species | Runella slithyformis (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||||||||||||||
Authors | Wang, H. / Sun, X.M. / Saburi, W. / Yu, J. / Yao, M. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h1n.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h1n.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 8h1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/8h1n ftp://data.pdbj.org/pub/pdb/validation_reports/h1/8h1n | HTTPS FTP |
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-Related structure data
Related structure data | 8h1kC 8h1lC 8h1mC 3vw5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Runella slithyformis (bacteria) / Gene: Runsl_4512 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U4E834 | ||||
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#2: Sugar | ChemComp-SOR / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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