2RCV | pdb_00002rcv

Crystal structure of the Bacillus subtilis superoxide dismutase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.230 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structure of Bacillus subtilis superoxide dismutase.

Liu, P.Ewis, H.E.Huang, Y.J.Lu, C.D.Tai, P.C.Weber, I.T.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 1003-1007

  • DOI: https://doi.org/10.1107/S1744309107054127
  • Primary Citation Related Structures: 
    2RCV

  • PubMed Abstract: 

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 A resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two beta-strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.


  • Organizational Affiliation
    • Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA.

Macromolecule Content 

  • Total Structure Weight: 181.24 kDa 
  • Atom Count: 13,464 
  • Modeled Residue Count: 1,591 
  • Deposited Residue Count: 1,616 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Superoxide dismutase [Mn]
A, B, C, D, E
A, B, C, D, E, F, G, H
202Bacillus subtilisMutation(s): 0 
Gene Names: sodAyqgD
EC: 1.15.1.1
UniProt
Find proteins for P54375 (Bacillus subtilis (strain 168))
Explore P54375 
Go to UniProtKB:  P54375
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54375
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.230 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.369α = 99.13
b = 84.034β = 105.98
c = 91.951γ = 105.58
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description