6ZS1 | pdb_00006zs1

Chaetomium thermophilum CuZn-superoxide dismutase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZS1

This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a Cu,Zn Superoxide Dismutase From the Thermophilic Fungus Chaetomium thermophilum.

Mohsin, I.Zhang, L.Q.Li, D.C.Papageorgiou, A.C.

(2021) Protein Pept Lett 28: 1043-1053

  • DOI: https://doi.org/10.2174/0929866528666210316104919
  • Primary Citation Related Structures: 
    6ZS1

  • PubMed Abstract: 

    Thermophilic fungi have recently emerged as a promising source of thermostable enzymes. Superoxide dismutases are key antioxidant metalloenzymes with promising therapeutic effects in various diseases, both acute and chronic. However, structural heterogeneity and low thermostability limit their therapeutic efficacy. Although several studies from hypethermophilic superoxide dismutases (SODs) have been reported, information about Cu,Zn-SODs from thermophilic fungi is scarce. Chaetomium thermophilum is a thermophilic fungus that could provide proteins with thermophilic properties. The enzyme was expressed in Pichia pastoris cells and crystallized using the vapor-diffusion method. X-ray data were collected, and the structure was determined and refined to 1.56 Å resolution. Structural analysis and comparisons were carried out. The presence of 8 molecules (A through H) in the asymmetric unit resulted in four different interfaces. Molecules A and F form the typical homodimer which is also found in other Cu,Zn- SODs. Zinc was present in all subunits of the structure while copper was found in only four subunits with reduced occupancy (C, D, E and F). The ability of the enzyme to form oligomers and the elevated Thr:Ser ratio may be contributing factors to its thermal stability. Two hydrophobic residues that participate in interface formation and are not present in other CuZn-SODs may play a role in the formation of new interfaces and the oligomerization process. The CtSOD crystal structure reported here is the first Cu,Zn-SOD structure from a thermophilic fungus.


  • Organizational Affiliation
    • Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20521, Finland.

Macromolecule Content 

  • Total Structure Weight: 133.11 kDa 
  • Atom Count: 11,658 
  • Modeled Residue Count: 1,239 
  • Deposited Residue Count: 1,256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E
A, B, C, D, E, F, G, H
157Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0013440
EC: 1.15.1.1
UniProt
Find proteins for G0S1F8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S1F8 
Go to UniProtKB:  G0S1F8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S1F8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
AA [auth D]
J [auth A]
K [auth A]
NA [auth G]
P [auth B]
AA [auth D],
J [auth A],
K [auth A],
NA [auth G],
P [auth B],
QA [auth H],
X [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
HA [auth E],
KA [auth F],
SA [auth H],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
CA [auth E]
I [auth A]
IA [auth F]
MA [auth G]
O [auth B]
CA [auth E],
I [auth A],
IA [auth F],
MA [auth G],
O [auth B],
PA [auth H],
T [auth C],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
(Subject of Investigation/LOI)

Query on CU



Download:Ideal Coordinates CCD File
DA [auth E],
JA [auth F],
U [auth C],
Z [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BA [auth D]
EA [auth E]
FA [auth E]
GA [auth E]
L [auth A]
BA [auth D],
EA [auth E],
FA [auth E],
GA [auth E],
L [auth A],
LA [auth F],
M [auth A],
N [auth A],
OA [auth G],
Q [auth B],
R [auth B],
RA [auth H],
S [auth B],
TA [auth H],
V [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.11α = 90
b = 89.11β = 90
c = 310.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary