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- PDB-13aj: Structure of the HPII Catalase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 13aj
TitleStructure of the HPII Catalase from Escherichia coli
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Catalase / HPII / Heme / Reactive oxygen species / tetramer
Function / homologyCIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / :
Function and homology information
Biological speciesEscherichia coli 'BL21-GoldpLysS AG'
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsIarocci, J. / Song, M. / Guo, S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Sante (FRQS)359456 & 376506 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2024-04631 Canada
CitationJournal: To Be Published
Title: Adhesin-mediated co-purification of Escherichia coli HPII (KatE) Catalase revealed its cryo-EM structure
Authors: Iarocci, J. / Song, M. / Nadeau, J. / Wang, M. / Hancock, M. / Bui, K.H. / Guo, S.
History
DepositionApr 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Catalase
F: Catalase
G: Catalase
H: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,9928
Polymers318,4624
Non-polymers2,5304
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Catalase


Mass: 79615.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A061KVC0, catalase
#2: Chemical
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


Mass: 632.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: HPII catalase / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 9
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: TFS 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: 80 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7Cootmodel fitting
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28000 / Symmetry type: POINT

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