1DT0 | pdb_00001dt0

CLONING, SEQUENCE, AND CRYSTALLOGRAPHIC STRUCTURE OF RECOMBINANT IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS OVALIS

• PDB DOI: https://doi.org/10.2210/pdb1DT0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-10 Released: 2000-12-20 
• Deposition Author(s): Bond, C.J., Huang, J., Hajduk, R., Flick, K., Heath, P., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.290 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Cloning, sequence and crystallographic structure of recombinant iron superoxide dismutase from Pseudomonas ovalis.

Bond, C.J., Huang, J., Hajduk, R., Flick, K.E., Heath, P.J., Stoddard, B.L.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1359-1366

• PubMed: 11053832 
• DOI: https://doi.org/10.1107/s0907444900009537
• Primary Citation Related Structures: 
  1DT0


• PubMed Abstract: 
  

  The gene encoding the iron-dependent superoxide dismutase from Pseudomonas ovalis was cloned from a genomic library and sequenced. The ORF differs from the previously published protein sequence, which was used for the original structure determination, at 16 positions. The differences include three additional inserted residues, one deleted residue and 12 point substitutions. The gene was subcloned and the recombinant protein overexpressed, purified and crystallized in a trigonal space group. The structure was determined by molecular replacement and was refined to 2.1 A resolution.

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Organizational Affiliation: 
• Program in Biomolecular Structure and Design, University of Washington, USA.

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 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.9 kDa 
• Atom Count: 5,217 
• Modeled Residue Count: 589 
• Deposited Residue Count: 591 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE	A, B, C	197	Pseudomonas putida	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for P09223 (Pseudomonas putida) Explore P09223  Go to UniProtKB:  P09223

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.290 (Depositor) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.03	α = 90
b = 115.03	β = 90
c = 82.5	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-20 
Deposition Author(s): Bond, C.J., Huang, J., Hajduk, R., Flick, K., Heath, P., Stoddard, B.L.

Revision History  

• Version 1.0: 2000-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Experimental preparation
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations