7AZQ | pdb_00007azq

Crystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Fe

• PDB DOI: https://doi.org/10.2210/pdb7AZQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodobacter capsulatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-17 Released: 2021-12-01 
• Deposition Author(s): Ponce-Salvatierra, A., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of the cambialistic superoxide dismutase from Rhodobacter capsulatus.

Ponce-Salvatierra, A., Di Capua, C., Gonzalez, J., Cortez, N., Hermoso, J.A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.19 kDa 
• Atom Count: 3,317 
• Modeled Residue Count: 398 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Fe]	A, B [auth E]	199	Rhodobacter capsulatus	Mutation(s): 0  Gene Names: sodB, sod EC: 1.15.1.1
UniProt
Find proteins for O30970 (Rhodobacter capsulatus) Explore O30970  Go to UniProtKB:  O30970

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.79	α = 90
b = 162.79	β = 90
c = 43.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Ponce-Salvatierra, A., Hermoso, J.A.

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description