9T0L | pdb_00009t0l

Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution

• PDB DOI: https://doi.org/10.2210/pdb9T0L/pdb
• EM Map EMD-55404: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Agrobacterium radiobacter
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-17 Released: 2025-11-12 
• Deposition Author(s): Li, J., Henderson, R., Russo, C.J., Wilson, H., Chen, S.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Comparison of human and bacterial monofunctional catalase structures obtained by electron cryomicroscopy.

Slowik, D., Li, J., Wilson, H., Shtyrov, A., Chen, S., McMullan, G., Russo, C.J., Mushudov, G., Henderson, R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 56.49 kDa 
• Atom Count: 4,459 
• Modeled Residue Count: 480 
• Deposited Residue Count: 491 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A	491	Agrobacterium radiobacter	Mutation(s): 0  Gene Names: katH EC: 1.11.1.6
UniProt
Find proteins for B6EXX7 (Agrobacterium tumefaciens) Explore B6EXX7  Go to UniProtKB:  B6EXX7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	Servalcat	0.4.72

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Li, J., Henderson, R., Russo, C.J., Wilson, H., Chen, S.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_120117

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release