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- PDB-8uws: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 -

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Basic information

Entry
Database: PDB / ID: 8uws
TitleCryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
ComponentsBeta-xylosidase
KeywordsHYDROLASE / GH43 / Enterobacter / Beta-Xylosidase / EcXyl43
Function / homologyBeta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Beta-xylosidase
Function and homology information
Biological speciesEnterobacter hormaechei (CDC Enteric Group 75)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsBriganti, L. / Godoy, A.S. / Capetti, C.C.M. / Portugal, R.V. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
Authors: Briganti, L. / Godoy, A.S. / Polikarpov, I.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 15, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-xylosidase
D: Beta-xylosidase
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,1648
Polymers244,0044
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Beta-xylosidase


Mass: 61000.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter hormaechei (CDC Enteric Group 75)
Gene: FJMB80377_06160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9N7LAI9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric GH43 structure / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Enterobacter hormaechei (CDC Enteric Group 75)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 438836 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417710
ELECTRON MICROSCOPYf_angle_d0.56524198
ELECTRON MICROSCOPYf_dihedral_angle_d4.3472370
ELECTRON MICROSCOPYf_chiral_restr0.0452460
ELECTRON MICROSCOPYf_plane_restr0.0053151

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