2Q2L | pdb_00002q2l

Crystal Structure of Superoxide Dismutase from P. atrosanguina

• PDB DOI: https://doi.org/10.2210/pdb2Q2L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Potentilla atrosanguinea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-29 Released: 2008-03-25 
• Deposition Author(s): Manickam, Y., Gill, J., Mishra, P.C., Sharma, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.234 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 

Literature

SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution

Yogavel, M., Gill, J., Mishra, P.C., Sharma, A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 931-934

• PubMed: 17642520 
• DOI: https://doi.org/10.1107/S0907444907029174
• Primary Citation Related Structures: 
  2Q2L


• PubMed Abstract: 
  

  Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.

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Organizational Affiliation: 
• Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.83 kDa 
• Atom Count: 2,399 
• Modeled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide Dismutase	A, B	152	Potentilla atrosanguinea	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for B2CP37 (Potentilla atrosanguinea) Explore B2CP37  Go to UniProtKB:  B2CP37

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.234 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.14	α = 90
b = 64.12	β = 124.33
c = 63.62	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Manickam, Y., Gill, J., Mishra, P.C., Sharma, A.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary