6M30 | pdb_00006m30

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F

• PDB DOI: https://doi.org/10.2210/pdb6M30/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus equorum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-03-02 Released: 2021-02-10 
• Deposition Author(s): Retnoningrum, D.S., Yoshida, H., Razani, M.D., Meidianto, V.F., Hartanto, A., Artarini, A., Ismaya, W.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Unprecedented Role of The N73-F124 Pair in The Staphylococcus equorum MnSOD Activity.

Retnoningrum, D.S., Yoshida, H., Razani, M.D., Meidianto, V.F., Hartanto, A., Artarini, A., Ismaya, W.T.

(2021) Curr Enzym Inhib 

• DOI: https://doi.org/10.2174/1573408016999201027212952

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.54 kDa 
• Atom Count: 10,207 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D, E, F	205	Staphylococcus equorum	Mutation(s): 2  Gene Names: AST02_02815 EC: 1.15.1.1
UniProt
Find proteins for A0A1E5TT85 (Staphylococcus equorum) Explore A0A1E5TT85  Go to UniProtKB:  A0A1E5TT85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.123	α = 90
b = 132.504	β = 110.67
c = 80.507	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Retnoningrum, D.S., Yoshida, H., Razani, M.D., Meidianto, V.F., Hartanto, A., Artarini, A., Ismaya, W.T.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description