1MA1 | pdb_00001ma1

Structure and properties of the atypical iron superoxide dismutase from Methanobacterium thermoautotrophicum

• PDB DOI: https://doi.org/10.2210/pdb1MA1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-07-31 Released: 2002-08-21 
• Deposition Author(s): Adams, J.J., Anderson, B.F., Renault, J.P., Verchere-Beaur, C., Morgenstern-Badarau, I., Jameson, G.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.247 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure and properties of the atypical iron superoxide dismutase from Methanobacterium thermoautotrophicum

Adams, J.J., Anderson, B.F., Renault, J.P., Verchere-Beaur, C., Morgenstern-Badarau, I., Jameson, G.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.11 kDa 
• Atom Count: 10,460 
• Modeled Residue Count: 1,206 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
superoxide dismutase	A, B, C, D, E, F	205	Methanothermobacter thermautotrophicus	Mutation(s): 0  Gene Names: SODF EC: 1.15.1.1
UniProt
Find proteins for P18868 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore P18868  Go to UniProtKB:  P18868

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.247 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.619	α = 90
b = 114.082	β = 94.95
c = 58.087	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-21 
Deposition Author(s): Adams, J.J., Anderson, B.F., Renault, J.P., Verchere-Beaur, C., Morgenstern-Badarau, I., Jameson, G.B.

Revision History  

• Version 1.0: 2002-08-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description