1Y67 | pdb_00001y67

Crystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb1Y67/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-03 Released: 2004-12-21 
• Deposition Author(s): Chan, S., Tanaka, S., Sawaya, M.R., Perry, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans

Chan, S., Tanaka, S., Sawaya, M.R., Perry, L.J.

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: 102.1 kDa 
• Atom Count: 6,965 
• Modeled Residue Count: 832 
• Deposited Residue Count: 916 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Manganese Superoxide dismutase	A, B, C, D	229	Deinococcus radiodurans	Mutation(s): 0  Gene Names: sodA EC: 1.15.1.1
UniProt
Find proteins for Q9RUV2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUV2  Go to UniProtKB:  Q9RUV2

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: 1.85 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.801	α = 90
b = 87.922	β = 91.14
c = 116.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Chan, S., Tanaka, S., Sawaya, M.R., Perry, L.J.

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description