5GKN | pdb_00005gkn

Catalase structure determined by electron crystallography of thin 3D crystals

• PDB DOI: https://doi.org/10.2210/pdb5GKN/pdb
• Entry: 5GKN supersedes: 3J7U

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2016-07-04 Released: 2016-10-26 
• Deposition Author(s): Yonekura, K.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.20 Å
• R-Value Free: 
  0.304 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Refinement of Cryo-EM Structures Using Scattering Factors of Charged Atoms

Yonekura, K., Maki-Yonekura, M.

(2016) J Appl Crystallogr 49: 1517-1523

• DOI: https://doi.org/10.1107/S1600576716011274

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)

Macromolecule Content 

• Total Structure Weight: 245.44 kDa 
• Atom Count: 16,548 
• Modeled Residue Count: 1,996 
• Deposited Residue Count: 2,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	527	Bos taurus	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus) Explore P00432  Go to UniProtKB:  P00432

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.20 Å
• R-Value Free:  0.304 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69	α = 90
b = 173.5	β = 90
c = 206	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
EDINT	data scaling
Modified version of phenix	phasing
Modified	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Yonekura, K.
• This entry supersedes: 3J7U

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Funding Organization	Location	Grant Number
	Japan	--

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description