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- PDB-4m81: The structure of E292S glycosynthase variant of exo-1,3-beta-gluc... -

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Basic information

Entry
Database: PDB / ID: 4m81
TitleThe structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with 1-fluoro-alpha-D-glucopyranoside (donor) and p-nitrophenyl beta-D-glucopyranoside (acceptor) at 1.86A resolution
ComponentsEXO-1,3-BETA-GLUCANASE
KeywordsHYDROLASE / TIM BARREL / GLYCOSIDE HYDROLASE FAMILY 5 / GLYCOSIDE HYDROLASE / CELL WALL HYDROLASE / GLYCOSYNTHASE / PROTEIN-CARBOHYDRATE INTERACTION
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
alpha-D-glucopyranosyl fluoride / 4-nitrophenyl beta-D-glucopyranoside / Glucan 1,3-beta-glucosidase / Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,2694
Polymers45,6931
Non-polymers5753
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.006, 64.202, 95.037
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: Sugar ChemComp-GLF / alpha-D-glucopyranosyl fluoride / 1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE / alpha-D-glucosyl fluoride / D-glucosyl fluoride / glucosyl fluoride


Type: D-saccharide / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp1fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-PNW / 4-nitrophenyl beta-D-glucopyranoside / 4'-NITROPHENYL-BETA-D-GLUCOPYRANOSIDE / 4-nitrophenyl beta-D-glucoside / 4-nitrophenyl D-glucoside / 4-nitrophenyl glucoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
4'-nitrophenyl-b-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 1.97 Å3/Da / Density % sol: 37.56 %
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: Jun 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→37.01 Å / Num. all: 28317 / Num. obs: 28249 / % possible obs: 90.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 15.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3304 / Rsym value: 0.527 / % possible all: 74

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Processing

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

1cz1


Resolution: 1.86→18.092 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1398 4.97 %RANDOM
Rwork0.1485 ---
obs0.1515 28109 90.13 %-
all-28249 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→18.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 39 492 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073378
X-RAY DIFFRACTIONf_angle_d1.0414615
X-RAY DIFFRACTIONf_dihedral_angle_d13.6621177
X-RAY DIFFRACTIONf_chiral_restr0.075468
X-RAY DIFFRACTIONf_plane_restr0.005603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8557-1.9220.2761150.20992036X-RAY DIFFRACTION70
1.922-1.99890.30861220.2162363X-RAY DIFFRACTION81
1.9989-2.08970.26581170.17362521X-RAY DIFFRACTION86
2.0897-2.19970.2141490.15712598X-RAY DIFFRACTION89
2.1997-2.33720.24071620.14692686X-RAY DIFFRACTION92
2.3372-2.51730.23221440.1462785X-RAY DIFFRACTION95
2.5173-2.76980.2121460.14732841X-RAY DIFFRACTION96
2.7698-3.16870.20311490.14622890X-RAY DIFFRACTION97
3.1687-3.98520.16551450.12282958X-RAY DIFFRACTION98
3.9852-18.09280.17971490.14183033X-RAY DIFFRACTION97

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