4BIM | pdb_00004bim

CATALASE 3 FROM NEUROSPORA CRASSA IN TETRAGONAL FORM EXPOSES A MODIFIED TETRAMERIC ORGANIZATION

• PDB DOI: https://doi.org/10.2210/pdb4BIM/pdb

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


• Deposited: 2013-04-11 Released: 2013-04-24 
• Deposition Author(s): Zarate-Romero, A., Rudino-Pinera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.304 (Depositor), 0.338 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.285 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

Literature

Conformational Stability and Crystal Packing: Polymorphism in Neurospora Crassa Cat-3

Zarate-Romero, A., Stojanoff, V., Rojas-Trejo, S.P., Hansberg, W., Rudino-Pinera, E.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 753

• PubMed: 23832201 
• DOI: https://doi.org/10.1107/S1744309113013468
• Primary Citation Related Structures: 
  3ZJ4, 3ZJ5, 4BIM


• PubMed Abstract: 
  

  Polymorphism is frequently observed from different crystallization conditions. In proteins, the effect on conformational variability is poorly documented, with only a few reported examples. Here, three polymorphic crystal structures determined for a large-subunit catalase, CAT-3 from Neurospora crassa, are reported. Two of them belonged to new space groups, P1 and P43212, and a third structure belonged to the same space group, P212121, as the previously deposited 2.3 Å resolution structure (PDB entry 3ej6), but had a higher resolution (1.95 Å). Comparisons between these polymorphic structures highlight the conformational stability of tetrameric CAT-3 and reveal a distortion in the tetrameric structure that has not previously been described.

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Organizational Affiliation: 
• Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Chamilpa, 62210 Cuernavaca, MOR, Mexico. [e-mail]

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 332.67 kDa 
• Atom Count: 21,809 
• Modeled Residue Count: 2,721 
• Deposited Residue Count: 2,984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE 3	A, B, C, D	746	Neurospora crassa	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for Q9C169 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q9C169  Go to UniProtKB:  Q9C169

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	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: 2.95 Å
• R-Value Free:  0.304 (Depositor), 0.338 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.285 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.508	α = 90
b = 207.508	β = 90
c = 137.041	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Zarate-Romero, A., Rudino-Pinera, E.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description