5N56 | pdb_00005n56

Staphylococcus aureus Mn-dependent superoxide dismutase SodA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.150 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

A charge polarization model for the metal-specific activity of superoxide dismutases.

Barwinska-Sendra, A., Basle, A., Waldron, K.J., Un, S.

(2018) Phys Chem Chem Phys 20: 2363-2372

  • DOI: https://doi.org/10.1039/c7cp06829h
  • Primary Citation Related Structures: 
    5N56, 5N57

  • PubMed Abstract: 

    The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site 1 H- and 14 N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.

    • Organizational Affiliation: 
    • Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK. kevin.waldron@newcastle.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 45.59 kDa 
  • Atom Count: 3,344 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Mn/Fe] 1
A, B
199Staphylococcus aureus RF122Mutation(s): 0 
Gene Names: sodA, SAB1425c
EC: 1.15.1.1
UniProt
Find proteins for Q2YT26 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Explore Q2YT26 
Go to UniProtKB:  Q2YT26
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YT26
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.275α = 90
b = 68.356β = 99.45
c = 56.724γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--
Wellcome TrustUnited Kingdom098375/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description