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- PDB-4m82: The structure of E292S glycosynthase variant of exo-1,3-beta-gluc... -

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Basic information

Entry
Database: PDB / ID: 4m82
TitleThe structure of E292S glycosynthase variant of exo-1,3-beta-glucanase from Candida albicans complexed with p-nitrophenyl-gentiobioside (product) at 1.6A 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
beta-D-glucopyranose / Chem-NGB / Glucan 1,3-beta-glucosidase / Glucan 1,3-beta-glucosidase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.592 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.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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)46,4615
Polymers45,6931
Non-polymers7684
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.785, 64.333, 94.489
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-NGB / 4-nitrophenyl 6-O-beta-D-glucopyranosyl-beta-D-glucopyranoside / P-NITROPHENYL-GENTIOBIOSIDE


Type: D-saccharide / Mass: 463.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H25NO13
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 37.09 %
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: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→39.44 Å / Num. all: 48332 / Num. obs: 48285 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.027 / Rsym value: 0.027 / Net I/σ(I): 39.2
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / Num. unique all: 6562 / Rsym value: 0.212 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CrystalCleardata 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: 1.592→28.218 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2436 5.05 %RANDOM
Rwork0.1474 ---
obs0.1492 48214 98.98 %-
all-48332 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.592→28.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 52 486 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063429
X-RAY DIFFRACTIONf_angle_d1.0784697
X-RAY DIFFRACTIONf_dihedral_angle_d14.0891217
X-RAY DIFFRACTIONf_chiral_restr0.073481
X-RAY DIFFRACTIONf_plane_restr0.005614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5918-1.62430.23841340.18792208X-RAY DIFFRACTION84
1.6243-1.65960.22411410.17762676X-RAY DIFFRACTION100
1.6596-1.69820.22171520.17042673X-RAY DIFFRACTION100
1.6982-1.74070.1971400.16642718X-RAY DIFFRACTION100
1.7407-1.78780.20991310.16042689X-RAY DIFFRACTION100
1.7878-1.84030.20151490.16032694X-RAY DIFFRACTION100
1.8403-1.89970.22031500.15052681X-RAY DIFFRACTION100
1.8997-1.96760.21341210.14992708X-RAY DIFFRACTION100
1.9676-2.04640.21071680.15132678X-RAY DIFFRACTION100
2.0464-2.13950.18961350.14592702X-RAY DIFFRACTION100
2.1395-2.25220.18071510.14992718X-RAY DIFFRACTION100
2.2522-2.39330.19531370.14352721X-RAY DIFFRACTION100
2.3933-2.57790.19221280.15562754X-RAY DIFFRACTION100
2.5779-2.83720.18841570.1472716X-RAY DIFFRACTION100
2.8372-3.24720.1711380.1462766X-RAY DIFFRACTION100
3.2472-4.08910.15781510.12672785X-RAY DIFFRACTION100
4.0891-28.22260.15331530.14252891X-RAY DIFFRACTION99

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