3LSU | pdb_00003lsu

Crystal Structure of SOD2 from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3LSU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2010-02-12 Released: 2011-02-23 
• Deposition Author(s): Sheng, Y., Cascio, D., Valentine, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of SOD2 from Saccharomyces cerevisiae

Sheng, Y., Cascio, D., Valentine, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 94.77 kDa 
• Atom Count: 7,111 
• Modeled Residue Count: 826 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn], mitochondrial	A, B, C, D	207	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SOD2, YHR008C EC: 1.15.1.1
UniProt
Find proteins for P00447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00447  Go to UniProtKB:  P00447

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B], J [auth C], L [auth D], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	E [auth A], F [auth B], H [auth C], K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C, D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.657	α = 109.36
b = 64.933	β = 106.35
c = 66.55	γ = 109.68

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Sheng, Y., Cascio, D., Valentine, J.S.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description