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)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9T0L

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6EXX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.