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Yorodumi- PDB-3o6a: F144Y/F258Y Double Mutant of Exo-beta-1,3-glucanase from Candida ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o6a | ||||||
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Title | F144Y/F258Y Double Mutant of Exo-beta-1,3-glucanase from Candida albicans at 2 A | ||||||
Components | Glucan 1,3-beta-glucosidase | ||||||
Keywords | HYDROLASE / TIM Barrel / Gycoside hydrolase family 5 / Glycoside hydrolase / Secreted / Cell wall | ||||||
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 / fungal-type cell wall organization / glucan catabolic process / 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 / fungal-type cell wall organization / glucan catabolic process / 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: 2 Å | ||||||
Authors | Nakatani, Y. / Cutfield, S.M. / Cutfield, J.F. | ||||||
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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o6a.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o6a.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o6a_validation.pdf.gz | 421.6 KB | Display | wwPDB validaton report |
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Full document | 3o6a_full_validation.pdf.gz | 422.6 KB | Display | |
Data in XML | 3o6a_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3o6a_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/3o6a ftp://data.pdbj.org/pub/pdb/validation_reports/o6/3o6a | HTTPS FTP |
-Related structure data
Related structure data | 2pc8C 2pf0C 3n9kC 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: 45767.348 Da / Num. of mol.: 1 / Mutation: F144Y, F258Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: XOG / Plasmid: PPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P29717, glucan 1,3-beta-glucosidase |
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#2: Water | ChemComp-HOH / |
Sequence 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: 1.96 Å3/Da / Density % sol: 37.27 % |
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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% PEG 8000, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.23 Å / Num. all: 40821 / Num. obs: 25035 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3592 / Rsym value: 0.43 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CZ1 Resolution: 2→38.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.704 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.213 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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