3J7B

Catalase solved at 3.2 Angstrom resolution by MicroED

• PDB DOI: https://doi.org/10.2210/pdb3J7B/pdb
• EM Map EMD-6314: EMDB EMDataResource

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


• Deposited: 2014-06-09 Released: 2014-10-08 
• Deposition Author(s): Nannenga, B.L., Shi, D., Hattne, J., Reyes, F.E., Gonen, T.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.20 Å
• R-Value Free: 
  0.308 (Depositor) 
• R-Value Work: 
  0.262 (Depositor) 
• R-Value Observed: 
  0.264 (Depositor) 

Literature

Structure of catalase determined by MicroED.

Nannenga, B.L., Shi, D., Hattne, J., Reyes, F.E., Gonen, T.

(2014) Elife 3: e03600-e03600

• PubMed: 25303172 
• DOI: https://doi.org/10.7554/eLife.03600
• Primary Citation of Related Structures:  
  3J7B


• PubMed Abstract: 
  

  MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

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Organizational Affiliation: 

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.

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: 16,432 
• Modelled 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:  0.308 (Depositor) 
• R-Value Work:  0.262 (Depositor) 
• R-Value Observed: 0.264 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/186

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.842	α = 90
b = 172.081	β = 90
c = 182.067	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Nannenga, B.L., Shi, D., Hattne, J., Reyes, F.E., Gonen, T.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Other
• Version 1.2: 2022-08-24
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection