4OJA | pdb_00004oja

Structure of Hydra Cu-Zn superoxide dismutase

• PDB DOI: https://doi.org/10.2210/pdb4OJA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Hydra vulgaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-21 Released: 2015-01-28 
• Deposition Author(s): Anupama, A., Ramaswamy, S., Sai Sudha, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure of a Cu-Zn Superoxide dismutase at an evolutionary crossroad.

Subhadra, D., Anupama, A., Chirag, J., Ramaswamy, S., Sai Sudha, P.

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: 18.03 kDa 
• Atom Count: 1,163 
• Modeled Residue Count: 149 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A	170	Hydra vulgaris	Mutation(s): 0  Gene Names: SOD1, SodA EC: 1.15.1.1
UniProt
Find proteins for I3V7W8 (Hydra vulgaris) Explore I3V7W8  Go to UniProtKB:  I3V7W8

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: 2.28 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.36	α = 90
b = 70.36	β = 90
c = 148.96	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
PROCESS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Anupama, A., Ramaswamy, S., Sai Sudha, P.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary