4BR6 | pdb_00004br6

Crystal structure of Chaetomium thermophilum MnSOD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.178 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.120 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4BR6

This is version 1.3 of the entry. See complete history

Literature

Crystal Structure and Biochemical Characterization of a Manganese Superoxide Dismutase from Chaetomium Thermophilum.

Haikarainen, T.Frioux, C.Zhnag, L.Li, D.Papageorgiou, A.C.

(2014) Biochim Biophys Acta 1844: 422

  • DOI: https://doi.org/10.1016/j.bbapap.2013.11.014
  • Primary Citation Related Structures: 
    4BR6

  • PubMed Abstract: 

    A manganese superoxide dismutase from the thermophilic fungus Chaetomium thermophilum (CtMnSOD) was expressed in Pichia pastoris and purified to homogeneity. Its optimal temperature was 60°C with approximately 75% of its activity retained after incubation at 70°C for 60min. Recombinant yeast cells carrying C. thermophilum mnsod gene exhibited higher stress resistance to salt and oxidative stress-inducing agents than control yeast cells. In an effort to provide structural insights, CtMnSOD was crystallized and its structure was determined at 2.0Å resolution. The overall architecture of CtMnSOD was found similar to other MnSODs with highest structural similarities obtained against a MnSOD from the thermotolerant fungus Aspergillus fumigatus. In order to explain its thermostability, structural and sequence analysis of CtMnSOD with other MnSODs was carried out. An increased number of charged residues and an increase in the number of intersubunit salt bridges and the Thr:Ser ratio were identified as potential reasons for the thermostability of CtMnSOD.


  • Organizational Affiliation
    • Turku Centre for Biotechnology, University of Turku, BioCity, Turku 20521, Finland; Åbo Akademi University, BioCity, Turku 20521, Finland.

Macromolecule Content 

  • Total Structure Weight: 87.9 kDa 
  • Atom Count: 7,483 
  • Modeled Residue Count: 787 
  • Deposited Residue Count: 788 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE
A, B, C, D
197Thermochaetoides thermophilaMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for F8V325 (Thermochaetoides thermophila)
Explore F8V325 
Go to UniProtKB:  F8V325
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8V325
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN3

Query on MN3



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
K [auth C],
N [auth D]
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
L [auth C]
M [auth C]
F [auth A],
G [auth A],
H [auth A],
L [auth C],
M [auth C],
O [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.178 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.120 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.14α = 90
b = 69.14β = 90
c = 300.43γ = 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: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description