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Yorodumi- PDB-2pb1: Exo-B-(1,3)-Glucanase from Candida Albicans in complex with unhyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pb1 | ||||||
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Title | Exo-B-(1,3)-Glucanase from Candida Albicans in complex with unhydrolysed and covalently linked 2,4-dinitrophenyl-2-deoxy-2-fluoro-B-D-glucopyranoside at 1.9 A | ||||||
Components | Hypothetical protein XOG1Hypothesis | ||||||
Keywords | HYDROLASE / EXO-GLUCANASE / CANDIDA ALBICANS / MECHANISM-BASED INHIBITOR | ||||||
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: 1.9 Å | ||||||
Authors | Cutfield, S.M. / Cutfield, J.F. / Davies, G.J. / Sullivan, P.A. | ||||||
Citation | Journal: To be Published Title: Exo-B-(1,3)-Glucanase from Candida Albicans in complex with unhydrolysed and covalently linked 2,4-dinitrophenyl-2-deoxy-2-fluoro-B-D-glucopyranoside at 1.9 A Authors: Cutfield, S.M. / Cutfield, J.F. / Davies, G.J. / Sullivan, P.A. #1: Journal: J.Mol.Biol. 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 hydrolases. 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 | 2pb1.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pb1.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/2pb1 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pb1 | HTTPS FTP |
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-Related structure data
Related structure data | 1eqpS S: Starting model for refinement |
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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: 45792.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: EXG / Plasmid: pEMBLYEX4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AWY-1 References: UniProt: Q5AIZ3, UniProt: P29717*PLUS, glucan 1,3-beta-glucosidase |
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#2: Sugar | ChemComp-G2F / |
#3: Sugar | ChemComp-NFG / |
#4: 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: 2.09 Å3/Da / Density % sol: 41.08 % |
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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: Feb 6, 1997 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→20 Å / Num. all: 30898 / Num. obs: 28359 / % possible obs: 91.6 % / Rmerge(I) obs: 0.047 / Χ2: 0.994 / Net I/σ(I): 14.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EQP Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.32 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.116 / 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: 20.534 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.92 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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