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- PDB-8exd: Crystal structure of Aspergillus fumigatus sterylglucosidase A -

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Basic information

Entry
Database: PDB / ID: 8exd
TitleCrystal structure of Aspergillus fumigatus sterylglucosidase A
ComponentsSterylglucosidase A (SglA)
KeywordsHYDROLASE / glucosidase / sterylglucosidase
Function / homology
Function and homology information


ergosteryl 3-beta-D-glucoside catabolic process / steryl-beta-glucosidase activity / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / polysaccharide catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycosyl hydrolase, putative
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPereira de Sa, N. / Del Poeta, M. / Airola, M.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 AI125770 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35GM128666 United States
CitationJournal: Mbio / Year: 2023
Title: Targeting Sterylglucosidase A to Treat Aspergillus fumigatus Infections.
Authors: Pereira de Sa, N. / Jayanetti, K. / Rendina, D. / Clement, T. / Soares Brauer, V. / Mota Fernandes, C. / Ojima, I. / Airola, M.V. / Del Poeta, M.
History
DepositionOct 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sterylglucosidase A (SglA)
B: Sterylglucosidase A (SglA)
C: Sterylglucosidase A (SglA)
D: Sterylglucosidase A (SglA)


Theoretical massNumber of molelcules
Total (without water)353,3144
Polymers353,3144
Non-polymers00
Water00
1
A: Sterylglucosidase A (SglA)


Theoretical massNumber of molelcules
Total (without water)88,3281
Polymers88,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sterylglucosidase A (SglA)


Theoretical massNumber of molelcules
Total (without water)88,3281
Polymers88,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sterylglucosidase A (SglA)


Theoretical massNumber of molelcules
Total (without water)88,3281
Polymers88,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sterylglucosidase A (SglA)


Theoretical massNumber of molelcules
Total (without water)88,3281
Polymers88,3281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.731, 112.792, 139.102
Angle α, β, γ (deg.)90.000, 102.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sterylglucosidase A (SglA)


Mass: 88328.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_3G08820 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q4WXA7

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% polyethylene glycol (PEG) 3350, 0.2 M magnesium acetate pH 4.5

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.8→76.95 Å / Num. obs: 32036 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
3.8-4.0170.844666199.8
12.02-76.956.90.0661064199.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LPQ

7lpq


Resolution: 3.8→58.21 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3236 3109 5 %
Rwork0.2785 59081 -
obs0.2807 31957 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.94 Å2 / Biso mean: 177.2008 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.8→58.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21118 0 0 0 21118
Num. residues----2607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.860.42441750.36832682285799
3.86-3.920.40571080.362681278999
3.92-3.990.37791610.3582716287799
3.99-4.060.391190.32832698281799
4.06-4.140.44821530.32872678283199
4.14-4.230.34081500.33242650280098
4.23-4.320.37591590.31312660281998
4.32-4.420.35811150.3192584269996
4.42-4.530.34951310.29922582271394
4.53-4.650.31431280.29772746287499
4.65-4.790.34581540.302526692823100
4.79-4.940.31881310.289727392870100
4.94-5.120.33091510.293927602911100
5.12-5.320.28721650.296326542819100
5.32-5.560.30031330.283127472880100
5.57-5.860.33441370.290226842821100
5.86-6.220.36421370.30082754289199
6.23-6.70.31471430.29522656279999
6.7-7.380.32071400.26312698283899
7.38-8.440.26711320.23932674280698
8.44-10.630.29671430.22962682282598
10.63-58.210.30021440.23822687283199

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