4FFK | pdb_00004ffk

X-ray structure of iron superoxide dismutase from Acidilobus saccharovorans

• PDB DOI: https://doi.org/10.2210/pdb4FFK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acidilobus saccharovorans 345-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-01 Released: 2012-06-27 
• Deposition Author(s): Safonova, T.N., Slutskaya, E.S., Dorovatovsky, P.V., Bezsudnova, E.Yu., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O., Polyakov, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of iron superoxide dismutase from Acidilobus saccharovorans

Safonova, T.N., Slutskaya, E.S., Dorovatovsky, P.V., Bezsudnova, E.Yu., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O., Polyakov, K.M.

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: 25.45 kDa 
• Atom Count: 1,840 
• Modeled Residue Count: 212 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A	223	Acidilobus saccharovorans 345-15	Mutation(s): 0  Gene Names: ASAC_0498 EC: 1.15.1.1
UniProt
Find proteins for D9Q0R7 (Acidilobus saccharovorans (strain DSM 16705 / JCM 18335 / VKM B-2471 / 345-15)) Explore D9Q0R7  Go to UniProtKB:  D9Q0R7

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.44	α = 90
b = 99.44	β = 90
c = 81.4	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Safonova, T.N., Slutskaya, E.S., Dorovatovsky, P.V., Bezsudnova, E.Yu., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Skryabin, K.G., Popov, V.O., Polyakov, K.M.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Database references, Refinement description, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description