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- PDB-2pf0: F258I mutant of EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS at 1.9 A -

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Basic information

Entry
Database: PDB / ID: 2pf0
TitleF258I mutant of EXO-B-(1,3)-GLUCANASE FROM CANDIDA ALBICANS at 1.9 A
ComponentsHypothetical protein XOG1Hypothesis
KeywordsHYDROLASE / 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
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 / Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCutfield, 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
DepositionApr 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein XOG1


Theoretical massNumber of molelcules
Total (without water)45,7581
Polymers45,7581
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.330, 65.390, 96.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein XOG1 / Hypothesis


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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 8000, Hepes, CaCl2, pH 7.3, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→32.65 Å / Num. all: 30774 / Num. obs: 30432 / % possible obs: 98.89 % / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1256 4.1 %RANDOM
Rwork0.134 ---
obs0.135 30432 98.89 %-
all-30774 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.389 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 334 3545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213335
X-RAY DIFFRACTIONr_bond_other_d0.0010.022142
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.8974555
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0025173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23925190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9091513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.2220.2622
X-RAY DIFFRACTIONr_nbd_other0.1970.22162
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21642
X-RAY DIFFRACTIONr_nbtor_other0.0880.21505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.221
X-RAY DIFFRACTIONr_mcbond_it1.0071.51993
X-RAY DIFFRACTIONr_mcbond_other0.2431.5805
X-RAY DIFFRACTIONr_mcangle_it1.55623145
X-RAY DIFFRACTIONr_scbond_it2.48631602
X-RAY DIFFRACTIONr_scangle_it3.7034.51410
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 75 -
Rwork0.2 2047 -
obs-2122 95.33 %

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