1AVM | pdb_00001avm

THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE

• PDB DOI: https://doi.org/10.2210/pdb1AVM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Propionibacterium freudenreichii subsp. shermanii
• Mutation(s): No 


• Deposited: 1997-09-17 Released: 1998-03-18 
• Deposition Author(s): Schmidt, M., Parak, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.198 (Depositor) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

The Structure of the Azide Coordinated Superoxide Dismutase of P. Shermanii Investigated by X-Ray Structure Analysis, Exafs, Mossbauer-and Epr Spectroscopy

Schmidt, M., Scherk, C., Iakovleva, O., Nolting, H.F., Meier, B., Parak, F.

(1998) Inorganica Chim Acta 275-276: 65-72

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.51 kDa 
• Atom Count: 3,640 
• Modeled Residue Count: 402 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE	A, B	201	Propionibacterium freudenreichii subsp. shermanii	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for P80293 (Propionibacterium freudenreichii subsp. shermanii) Explore P80293  Go to UniProtKB:  P80293

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
AZI	D [auth A], F [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.198 (Depositor) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.68	α = 90
b = 85.42	β = 90
c = 108.76	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SAINT	data reduction
SAINT	data scaling
CCP4	data scaling
SCALA	data scaling
TRUNCATE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-18 
Deposition Author(s): Schmidt, M., Parak, F.

Revision History  

• Version 1.0: 1998-03-18
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other, Refinement description
• Version 1.5: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.6: 2024-05-22
  Changes: Data collection