6JOV | pdb_00006jov

Crystal structure of a hypothetical Fe Superoxide dismutase

• PDB DOI: https://doi.org/10.2210/pdb6JOV/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-23 Released: 2020-01-29 
• Deposition Author(s): Bose, S., Purushothaman, S.S., Subramanian, R.
• Funding Organization(s): Department of Biotechnology (India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a hypothetical Fe Superoxide dismutase

Ashok, A., Bose, S., Jain, C., Purushothaman, S.S., Subramanian, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 102.25 kDa 
• Atom Count: 6,843 
• Modeled Residue Count: 790 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-Superoxide dismutase	A, B, C, D	219	synthetic construct	Mutation(s): 0  EC: 1.15.1.1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	IA [auth D], N [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	F [auth A], JA [auth D]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	G [auth A], H [auth A], O [auth B], P [auth B], X [auth C], Y [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	AA [auth C], BA [auth C], CA [auth C], I [auth A], J [auth A], KA [auth D], Q [auth B], R [auth B], S [auth B], Z [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	DA [auth C], EA [auth C], FA [auth C], GA [auth C], K [auth A], L [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FE	E [auth A], HA [auth D], M [auth B], W [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.018	α = 82.28
b = 55.088	β = 89.61
c = 74.623	γ = 68.49

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Bose, S., Purushothaman, S.S., Subramanian, R.

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Funding Organization	Location	Grant Number
Department of Biotechnology (India)	India	--

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description