4YIP | pdb_00004yip

X-ray structure of the iron/manganese cambialistic superoxide dismutase from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb4YIP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-02 Released: 2016-01-13 
• Deposition Author(s): Russo Krauss, I., Merlino, A., Pica, A., Sica, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases

Russo Krauss, I., Merlino, A., Pica, A., Rullo, R., Bertoni, A., Capasso, A., Amato, M., Riccitiello, F., De Vendittis, E., Sica, F.

(2015) RSC Adv 5: 87876-87887

• DOI: https://doi.org/10.1039/C5RA13559A

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: 94.59 kDa 
• Atom Count: 6,699 
• Modeled Residue Count: 810 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn/Fe]	A, B, C, D	210	Streptococcus mutans	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for P09738 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore P09738  Go to UniProtKB:  P09738

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.964	α = 90
b = 82.879	β = 94.25
c = 72.779	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Russo Krauss, I., Merlino, A., Pica, A., Sica, F.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description