2A03 | pdb_00002a03

Superoxide dismutase protein from plasmodium berghei

• PDB DOI: https://doi.org/10.2210/pdb2A03/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium berghei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-15 Released: 2005-06-21 
• Deposition Author(s): Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Hypothetical protein from plasmodium berghei

Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.43 kDa 
• Atom Count: 3,421 
• Modeled Residue Count: 394 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-superoxide dismutase homolog	A, B	206	Plasmodium berghei	Mutation(s): 0  Gene Names: PB000490.02.0 EC: 1.15.1.1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.111	α = 90
b = 105.111	β = 90
c = 207.935	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Holmes, M.A., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2005-06-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, 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