3JS4 | pdb_00003js4

Crystal structure of iron superoxide dismutase from Anaplasma phagocytophilum

• PDB DOI: https://doi.org/10.2210/pdb3JS4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Anaplasma phagocytophilum str. HZ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-09 Released: 2009-09-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.206 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Iron superoxide dismutase from Anaplasma phagocytophilum

Edwards, T.E., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 102.23 kDa 
• Atom Count: 7,184 
• Modeled Residue Count: 826 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D	227	Anaplasma phagocytophilum str. HZ	Mutation(s): 0  Gene Names: sodB, APH_0371 EC: 1.15.1.1
UniProt
Find proteins for Q2GKX4 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GKX4  Go to UniProtKB:  Q2GKX4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.206 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.66	α = 102.09
b = 66.6	β = 104.83
c = 85.44	γ = 88.58

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description