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Yorodumi- PDB-2pf0: F258I mutant of EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS at 1.9 A -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pf0 | ||||||
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Title | F258I mutant of EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS at 1.9 A | ||||||
Components | Hypothetical protein XOG1Hypothesis | ||||||
Keywords | HYDROLASE / EXO-GLUCANASE / CANDIDA ALBICANS / CARBOHYDRATE BINDING / AROMATIC ENTRANCEWAY | ||||||
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: 1.9 Å | ||||||
Authors | Cutfield, S.M. / Cutfield, J.F. / Patrick, W.M. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: Carbohydrate binding sites in Candida albicans exo-beta-1,3-glucanase and the role of the Phe-Phe 'clamp' at the active site entrance. Authors: Patrick, W.M. / Nakatani, Y. / Cutfield, S.M. / Sharpe, M.L. / Ramsay, R.J. / Cutfield, J.F. #1: Journal: J.Mol.Biol. / Year: 1999 Title: THE STRUCTURE OF THE EXO-BETA-(1,3)-GLUCANASE FROM CANDIDA ALBICANS IN NATIVE AND BOUND FORMS: RELATIONSHIP BETWEEN a POCKET AND GROOVE IN FAMILY 5 GLYCOSYL HYDROLASE. Authors: Cutfield, S.M. / Davies, G.J. / Murshudov, G. / Anderson, B.F. / Moody, P.C. / Sullivan, P.A. / Cutfield, J.F. | ||||||
History |
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Remark 999 | SEQUENCE DUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, RESIDUE 64 IS A SER WHEN FROM NATURAL ...SEQUENCE DUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, RESIDUE 64 IS A SER WHEN FROM NATURAL SOURCES, AND A LEU WHEN EXPRESSED IN SACCHAROMYCES CEREVISIAE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pf0.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pf0.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pf0 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pf0 | HTTPS FTP |
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-Related structure data
Related structure data | 2pc8C 3n9kC 3o6aC 1eqpS 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: 45758.383 Da / Num. of mol.: 1 / Mutation: F258I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: XOG1 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 References: UniProt: Q5AIZ3, UniProt: P29717*PLUS, glucan 1,3-beta-glucosidase |
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#2: Water | ChemComp-HOH / |
-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: 40.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG 8000, Hepes, CaCl2, pH 7.3, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32.65 Å / Num. all: 30774 / Num. obs: 30432 / % possible obs: 98.89 % / Rmerge(I) obs: 0.052 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EQP Resolution: 1.9→32.65 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.534 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.389 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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