3ZJ5

NEUROSPORA CRASSA CATALASE-3 EXPRESSED IN E. COLI, ORTHORHOMBIC FORM.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1107/S1744309113013468
  • Primary Citation of 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.


  • 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. anzaro@ibt.unam.mx


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATALASE-3
A, B, C, D
746Neurospora crassaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C169
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth C],
IA [auth D],
J [auth A],
T [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PG4
Query on PG4

Download Ideal Coordinates CCD File 
AA [auth C]
FA [auth D]
G [auth A]
GA [auth D]
H [auth A]
AA [auth C],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
P [auth B],
Q [auth B],
R [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TAR
Query on TAR

Download Ideal Coordinates CCD File 
U [auth C]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
AE3
Query on AE3

Download Ideal Coordinates CCD File 
HA [auth D],
I [auth A],
S [auth B]
2-(2-ETHOXYETHOXY)ETHANOL
C6 H14 O3
XXJWXESWEXIICW-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
E [auth A]
EA [auth D]
F [auth A]
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.52α = 90
b = 154.8β = 90
c = 160.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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