6QZM | pdb_00006qzm

H30 MnSOD-3 Mutant I

• PDB DOI: https://doi.org/10.2210/pdb6QZM/pdb

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


• Deposited: 2019-03-11 Released: 2020-02-19 
• Deposition Author(s): Bonetta, R., Trinh, C.H., Hunter, G.J., Hunter, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

H30 MnSOD-3 Mutant II

Bonetta, R., Trinh, C.H., Hunter, G.J., Hunter, T.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.87 kDa 
• Atom Count: 3,530 
• Modeled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn] 2, mitochondrial	A, B [auth C]	194	Caenorhabditis elegans	Mutation(s): 0  Gene Names: sod-3, C08A9.1 EC: 1.15.1.1
UniProt
Find proteins for P41977 (Caenorhabditis elegans) Explore P41977  Go to UniProtKB:  P41977

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth C], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], E [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.49	α = 90
b = 81.49	β = 90
c = 138.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Bonetta, R., Trinh, C.H., Hunter, G.J., Hunter, T.

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Structure summary
• Version 1.2: 2020-09-09
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2020-09-16
  Changes: Data collection
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description