3KKY

Structure of Manganese Superoxide Dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity

• PDB DOI: https://doi.org/10.2210/pdb3KKY/pdb

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


• Deposited: 2009-11-06 Released: 2010-11-03 
• Deposition Author(s): Govindasamy, L., Mikulski, R., McKenna, M.A., Silverman, D.N., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Structure of Manganese Superoxide dismutase from Deinococcus Radiodurans in the orthorhombic space group P212121: A case study of mistaken identity

Govindasamy, L., Mikulski, R., McKenna, M.A., Silverman, D.N., McKenna, R.

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: 47.12 kDa 
• Atom Count: 3,426 
• Modelled Residue Count: 408 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn]	A, B	211	Deinococcus radiodurans	Mutation(s): 0  Gene Names: sodA, DR_1279 EC: 1.15.1.1
UniProt
Find proteins for Q9RUV2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUV2  Go to UniProtKB:  Q9RUV2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.15	α = 90
b = 80.24	β = 90
c = 85.41	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Govindasamy, L., Mikulski, R., McKenna, M.A., Silverman, D.N., McKenna, R.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description