8Y17 | pdb_00008y17

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C

• PDB DOI: https://doi.org/10.2210/pdb8Y17/pdb

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


• Deposited: 2024-01-23 Released: 2025-01-29 
• Deposition Author(s): Putri, N.A., Fadillah, M.D., Yoshida, H., Retnoningrum, D.S., Artarini, A.A., Utami, R.A., Ismaya, W.T.
• Funding Organization(s): Program Penelitian, Pengabdian kepada Masyarakat dan Inovasi ITB (P3MI-ITB) Grant Scheme 2023

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C

Putri, N.A., Fadillah, M.D., Yoshida, H., Retnoningrum, D.S., Artarini, A.A., Utami, R.A., Ismaya, W.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.19 kDa 
• Atom Count: 6,443 
• Modeled Residue Count: 793 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D	205	Staphylococcus equorum	Mutation(s): 3  Gene Names: AST02_02815, M4L21_03170 EC: 1.15.1.1
UniProt
Find proteins for P0A0J3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0J3  Go to UniProtKB:  P0A0J3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38Y17

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.92	α = 90
b = 135.82	β = 102.74
c = 76.38	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Putri, N.A., Fadillah, M.D., Yoshida, H., Retnoningrum, D.S., Artarini, A.A., Utami, R.A., Ismaya, W.T.

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Funding Organization	Location	Grant Number
Program Penelitian, Pengabdian kepada Masyarakat dan Inovasi ITB (P3MI-ITB) Grant Scheme 2023	Indonesia	56/IT1/C10/SK-KU/2023

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release