3KBF | pdb_00003kbf

C. elegans Cu,Zn Superoxide Dismutase

• PDB DOI: https://doi.org/10.2210/pdb3KBF/pdb

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


• Deposited: 2009-10-20 Released: 2010-11-03 
• 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: 1.30 Å
• R-Value Free: 
  0.159 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

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: 16.35 kDa 
• Atom Count: 1,372 
• Modeled Residue Count: 156 
• 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.159 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.204	α = 90
b = 68.986	β = 90
c = 110.488	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: 2010-11-03 
Deposition Author(s): Pakhomova, O.N., Taylor, A.B., Schuermann, J.P., Culotta, V.L., Hart, P.J.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary