5SW4 | pdb_00005sw4

Crystal structure of native catalase-peroxidase KatG at pH8.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.171 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases.

Carpena, X.Wiseman, B.Deemagarn, T.Singh, R.Switala, J.Ivancich, A.Fita, I.Loewen, P.C.

(2005) EMBO Rep 6: 1156-1162

  • DOI: https://doi.org/10.1038/sj.embor.7400550
  • Primary Citation of Related Structures:  
    5SW4, 5SW5, 5SW6, 5SX0

  • PubMed Abstract: 

    The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.


  • Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg MB R3T 2N2, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase-peroxidase
A, B
728Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: katGBURPS1710b_3366
EC: 1.11.1.21
UniProt
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JNW6 
Go to UniProtKB:  Q3JNW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JNW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
TRS
Query on TRS

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXY
Query on OXY

Download Ideal Coordinates CCD File 
E [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TOX
Query on TOX
A, B
L-PEPTIDE LINKINGC11 H12 N2 O4TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.171 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.778α = 90
b = 115.981β = 90
c = 174.844γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2016-08-24 
  • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 2B2O

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaD9600

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Structure summary
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection