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- PDB-9t0m: Catalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom... -

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Basic information

Entry
Database: PDB / ID: 9t0m
TitleCatalase cryoEM structure from Micrococcus luteus at 1.9 Angstrom resolution.
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Catalase / NADPH / Protoporphyrin IX
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsLi, J. / Henderson, R. / Russo, C.J. / Wilson, H. / Chen, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
CitationJournal: To Be Published
Title: Comparison of human and bacterial monofunctional catalase structures obtained by electron cryomicroscopy.
Authors: Slowik, D. / Li, J. / Wilson, H. / Shtyrov, A. / Chen, S. / McMullan, G. / Russo, C.J. / Murshudov, G. / Henderson, R.
History
DepositionOct 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4613
Polymers58,0991
Non-polymers1,3622
Water7,602422
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,84312
Polymers232,3954
Non-polymers5,4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2generate(-1), (-1), (1)409.60001, 409.60001
3generate(1), (-1), (-1)409.60001, 409.60001
4generate(-1), (1), (-1)409.60001, 409.60001

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Components

#1: Protein Catalase


Mass: 58098.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Gene: katA / Plasmid: pUCIDT-Amp / Production host: Escherichia coli (E. coli) / References: UniProt: P29422, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
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: catalase with cofactor NADPH / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)Organism: Micrococcus luteus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pUCIDT-Amp
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1154 mMsodium chlorideNaCl1
210 mMsodium phosphateNaH2PO4-Na2HPO41
30.2 mMNicotinamide adenine diphosphateC21H30N7O1P31
45 mMCHAPSOC32H58N2O8S1
SpecimenConc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: HexAuFoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Only one optical group, with minimal beam tilt.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 155000 X / Calibrated magnification: 273437 X / Nominal defocus max: 18100 nm / Nominal defocus min: 11400 nm / Calibrated defocus min: 11400 nm / Calibrated defocus max: 18100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 3 sec. / Electron dose: 50.4 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 27182
Details: Images collected with AFIS with maximum image shift of 1.5 microns.
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2EPUimage acquisition
4RELION4CTF correction
7Coot0.9.8.93model fittingCryo-EM module
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13Servalcat0.4.72model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1046104
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 261172 / Algorithm: FOURIER SPACE / Details: Standard Relion gold standard. / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 1GZE

1gze


Pdb chain-ID: A / Accession code: 1GZE / Chain residue range: 7-505 / Details: The initial model was PDB entry 1GWE. / Pdb chain residue range: 7-505 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0068392882241910.0118391315
ELECTRON MICROSCOPYs_angle_nonh_d1.5681066157351.83868527

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