6LFK | pdb_00006lfk

Crystal structure of KatE from atypical E. coli

• PDB DOI: https://doi.org/10.2210/pdb6LFK/pdb
• Entry: 6LFK supersedes: 6JOA

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-03 Released: 2020-12-09 
• Deposition Author(s): Cho, H.S., Yoo, Y., Park, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of eKatE

Cho, H.S., Yoo, Y.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 340.25 kDa 
• Atom Count: 23,791 
• Modeled Residue Count: 2,883 
• Deposited Residue Count: 3,000 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
eKatE catalase	A, B, C, D	750	Escherichia coli	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for A0A6I8WFM0 (Escherichia coli M8) Explore A0A6I8WFM0  Go to UniProtKB:  A0A6I8WFM0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.585	α = 90
b = 178.935	β = 106.699
c = 107.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Cho, H.S., Yoo, Y., Park, J.B.
• This entry supersedes: 6JOA

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Changes: Advisory
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description