4C7U | pdb_00004c7u

Crystal structure of manganese superoxide dismutase from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4C7U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-25 Released: 2014-10-15 
• Deposition Author(s): Marques, A., Santos, S.P., Rosa, M., Carrondo, M.A., Abreu, I.A., Romao, C.V., Frazao, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.178 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the Arabidopsis Thaliana Manganese Superoxide Dismutase at 1.95 A Resolution

Marques, A., Santos, S.P., Rosa, M., Carrondo, M.A., Abreu, I.A., Romao, C.V., Frazao, C.

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 and generated by PISA (software)

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.17 kDa 
• Atom Count: 13,278 
• Modeled Residue Count: 1,618 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE [MN] 1, MITOCHONDRIAL	A, B, C, D, E, F, G, H	225	Arabidopsis thaliana	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for O81235 (Arabidopsis thaliana) Explore O81235  Go to UniProtKB:  O81235

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.178 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.952	α = 90.55
b = 59.181	β = 90.51
c = 107.98	γ = 89.85

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Marques, A., Santos, S.P., Rosa, M., Carrondo, M.A., Abreu, I.A., Romao, C.V., Frazao, C.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Data collection
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description