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- PDB-3o6a: F144Y/F258Y Double Mutant of Exo-beta-1,3-glucanase from Candida ... -

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Basic information

Entry
Database: PDB / ID: 3o6a
TitleF144Y/F258Y Double Mutant of Exo-beta-1,3-glucanase from Candida albicans at 2 A
ComponentsGlucan 1,3-beta-glucosidase
KeywordsHYDROLASE / TIM Barrel / Gycoside hydrolase family 5 / Glycoside hydrolase / Secreted / Cell wall
Function / homology
Function and homology information


single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / glucan catabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / cell-substrate adhesion ...single-species biofilm formation in or on host organism / glucan metabolic process / glucan 1,3-beta-glucosidase / single-species biofilm formation on inanimate substrate / adhesion of symbiont to host cell / glucan exo-1,3-beta-glucosidase activity / 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
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNakatani, Y. / Cutfield, S.M. / Cutfield, J.F.
CitationJournal: 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
DepositionJul 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucan 1,3-beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)45,7671
Polymers45,7671
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.573, 64.623, 94.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucan 1,3-beta-glucosidase / Exo-1 / 3-beta-glucanase


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsDUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, THIS POSITION IS A SER WHEN FROM NATURAL ...DUE TO ALTERNATIVE CODON USAGE BY CANDIDA ALBICANS, THIS POSITION IS A SER WHEN FROM NATURAL SOURCES, AND A LEU WHEN EXPRESSED IN SACCHAROMYCES CEREVISIAE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZ1

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
RfactorNum. reflection% reflectionSelection details
Rfree0.19966 1272 5.1 %RANDOM
Rwork0.15442 ---
obs0.1567 23701 99.98 %-
all-24973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.213 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-0 Å2-0 Å2
2---0.48 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 308 3524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213343
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.8994573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96724.921189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44415493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3461513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212700
X-RAY DIFFRACTIONr_mcbond_it0.7941.51960
X-RAY DIFFRACTIONr_mcangle_it1.38623155
X-RAY DIFFRACTIONr_scbond_it2.24231383
X-RAY DIFFRACTIONr_scangle_it3.3554.51415
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 98 -
Rwork0.24 1699 -
obs--100 %

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