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Yorodumi- PDB-4m80: The structure of E292S glycosynthase variant of exo-1,3-beta-gluc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m80 | ||||||
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Title | The structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans at 1.85A resolution | ||||||
Components | EXO-1,3-BETA-GLUCANASE | ||||||
Keywords | HYDROLASE / TIM BARREL / GLYCOSIDE HYDROLASE FAMILY 5 / GLYCOSIDE HYDROLASE / CELL WALL HYDROLASE / GLYCOSYNTHASE | ||||||
Function / homology | Function and homology information glucan metabolic process / single-species biofilm formation in or on host organism / glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / single-species biofilm formation on inanimate substrate / glucan catabolic process / fungal-type cell wall organization / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding ...glucan metabolic process / single-species biofilm formation in or on host organism / glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / single-species biofilm formation on inanimate substrate / glucan catabolic process / fungal-type cell wall organization / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion / cell adhesion molecule binding / extracellular vesicle / transferase activity / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.858 Å | ||||||
Authors | Nakatani, Y. / Cutfield, S.M. / Larsen, D.S. / Cutfield, J.F. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Major Change in Regiospecificity for the Exo-1,3-beta-glucanase from Candida albicans following Its Conversion to a Glycosynthase. Authors: Nakatani, Y. / Larsen, D.S. / Cutfield, S.M. / Cutfield, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m80.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m80.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 4m80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/4m80 ftp://data.pdbj.org/pub/pdb/validation_reports/m8/4m80 | HTTPS FTP |
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-Related structure data
Related structure data | 4m81C 4m82C 1cz1S S: Starting model for refinement C: citing same article (ref.) |
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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: 45693.312 Da / Num. of mol.: 1 / Fragment: EXO-1,3-BETA-GLUCANASE (unp residues 40-438) / Mutation: E292S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: CaO19.10507, XOG, XOG1 / Plasmid: PPIC9K / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115/KM71 References: UniProt: Q5AI63, UniProt: P29717*PLUS, glucan 1,3-beta-glucosidase |
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#2: Water | ChemComp-HOH / |
Nonpolymer details | DUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, THIS POSITION IS A SER WHEN FROM NATURAL ...DUE TO ALTERNATIV |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1M HEPES-KOH, 0.2M CACL2, 19% PEG8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 6, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→26.24 Å / Num. all: 33226 / Num. obs: 32719 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4253 / Rsym value: 0.364 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1CZ1 Resolution: 1.858→17.054 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.858→17.054 Å
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Refine LS restraints |
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LS refinement shell |
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