3KBE | pdb_00003kbe

Metal-free C. elegans Cu,Zn Superoxide Dismutase

• PDB DOI: https://doi.org/10.2210/pdb3KBE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2010-10-20 
• Deposition Author(s): Pakhomova, O.N., Taylor, A.B., Schuermann, J.P., Culotta, V.L., Hart, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure of C. elegans Cu,Zn Superoxide Dismutase

Pakhomova, O.N., Taylor, A.B., Schuermann, J.P., Culotta, V.L., Hart, P.J.

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: 16.13 kDa 
• Atom Count: 1,409 
• Modeled Residue Count: 140 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A	157	Caenorhabditis elegans	Mutation(s): 0  Gene Names: C15F1.7, sod-1 EC: 1.15.1.1
UniProt
Find proteins for P34697 (Caenorhabditis elegans) Explore P34697  Go to UniProtKB:  P34697

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.21	α = 90
b = 92.33	β = 90
c = 81.246	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Pakhomova, O.N., Taylor, A.B., Schuermann, J.P., Culotta, V.L., Hart, P.J.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary