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- PDB-4m80: The structure of E292S glycosynthase variant of exo-1,3-beta-gluc... -

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Basic information

Entry
Database: PDB / ID: 4m80
TitleThe structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans at 1.85A resolution
ComponentsEXO-1,3-BETA-GLUCANASE
KeywordsHYDROLASE / TIM BARREL / GLYCOSIDE HYDROLASE FAMILY 5 / GLYCOSIDE HYDROLASE / CELL WALL HYDROLASE / GLYCOSYNTHASE
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: 1.858 Å
AuthorsNakatani, Y. / Cutfield, S.M. / Larsen, D.S. / Cutfield, J.F.
CitationJournal: Biochemistry / Year: 2014
Title: Major Change in Regiospecificity for the Exo-1,3-beta-glucanase from Candida albicans following Its Conversion to a Glycosynthase.
Authors: Nakatani, Y. / Larsen, D.S. / Cutfield, S.M. / Cutfield, J.F.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXO-1,3-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)45,6931
Polymers45,6931
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.985, 65.331, 96.884
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 EXO-1,3-BETA-GLUCANASE


Mass: 45693.312 Da / Num. of mol.: 1 / Fragment: EXO-1,3-BETA-GLUCANASE (unp residues 40-438) / Mutation: E292S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: ATCC 10261 / Gene: CaO19.10507, XOG, XOG1 / Plasmid: PPIC9K / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115/KM71
References: UniProt: Q5AI63, UniProt: P29717*PLUS, glucan 1,3-beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1M HEPES-KOH, 0.2M CACL2, 19% PEG8000, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→26.24 Å / Num. all: 33226 / Num. obs: 32719 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4253 / Rsym value: 0.364 / % possible all: 89.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1CZ1

1cz1


Resolution: 1.858→17.054 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 1656 5.09 %RANDOM
Rwork0.139 ---
obs0.1409 32530 99.3 %-
all-32719 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.858→17.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 311 3517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073353
X-RAY DIFFRACTIONf_angle_d1.0594586
X-RAY DIFFRACTIONf_dihedral_angle_d13.631172
X-RAY DIFFRACTIONf_chiral_restr0.077460
X-RAY DIFFRACTIONf_plane_restr0.005606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8577-1.91230.26251380.21292449X-RAY DIFFRACTION96
1.9123-1.9740.22921240.21532511X-RAY DIFFRACTION98
1.974-2.04440.21811410.17362534X-RAY DIFFRACTION100
2.0444-2.12610.17191140.1422575X-RAY DIFFRACTION100
2.1261-2.22270.18641390.13622575X-RAY DIFFRACTION100
2.2227-2.33960.1761320.13582566X-RAY DIFFRACTION100
2.3396-2.48580.19341570.13972554X-RAY DIFFRACTION100
2.4858-2.6770.17261390.14122564X-RAY DIFFRACTION100
2.677-2.94520.18091350.14412605X-RAY DIFFRACTION100
2.9452-3.36850.19581380.13482614X-RAY DIFFRACTION100
3.3685-4.23320.13011550.10912629X-RAY DIFFRACTION100
4.2332-17.05450.15181440.11882698X-RAY DIFFRACTION98

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