3WNU

The crystal structure of catalase-peroxidase, KatG, from Synechococcus PCC7942


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 1.2 of the entry. See complete history


Literature

The 2.2 angstrom resolution structure of the catalase-peroxidase KatG from Synechococcus elongatus PCC7942.

Kamachi, S.Wada, K.Tamoi, M.Shigeoka, S.Tada, T.

(2014) Acta Crystallogr F Struct Biol Commun 70: 288-293

  • DOI: 10.1107/S2053230X14002052
  • Primary Citation of Related Structures:  
    3WNU

  • PubMed Abstract: 
  • The crystal structure of catalase-peroxidase from Synechococcus elongatus PCC7942 (SeKatG) was solved by molecular replacement and refined to an Rwork of 16.8% and an Rfree of 20.6% at 2.2 Å resolution. The asymmetric unit consisted of only one subunit of the catalase-peroxidase molecule, including a protoporphyrin IX haem moiety and two sodium ions ...

    The crystal structure of catalase-peroxidase from Synechococcus elongatus PCC7942 (SeKatG) was solved by molecular replacement and refined to an Rwork of 16.8% and an Rfree of 20.6% at 2.2 Å resolution. The asymmetric unit consisted of only one subunit of the catalase-peroxidase molecule, including a protoporphyrin IX haem moiety and two sodium ions. A typical KatG covalent adduct was formed, Met248-Tyr222-Trp94, which is a key structural element for catalase activity. The crystallographic equivalent subunit was created by a twofold symmetry operation to form the functional dimer. The overall structure of the dimer was quite similar to other KatGs. One sodium ion was located close to the proximal Trp314. The location and configuration of the proximal cation site were very similar to those of typical peroxidases such as ascorbate peroxidase. These features may provide a structural basis for the behaviour of the radical localization/delocalization during the course of the enzymatic reaction.


    Organizational Affiliation

    School of Graduate Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catalase-peroxidaseA720Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: katGSynpcc7942_1656
EC: 1.11.1.21
UniProt
Find proteins for Q31MN3 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore Q31MN3 
Go to UniProtKB:  Q31MN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ31MN3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEB
Query on HEB

Download Ideal Coordinates CCD File 
B [auth A]HEME B/C
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.744α = 90
b = 108.744β = 90
c = 202.888γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Other
  • Version 1.2: 2019-12-18
    Changes: Database references