6V59

Crystal structure of the diheme peroxidase BthA Y463M variant from Burkholderia thailandensis E264


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

A Stable Ferryl Porphyrin at the Active Site of Y463M BthA.

Rizzolo, K.Weitz, A.C.Cohen, S.E.Drennan, C.L.Hendrich, M.P.Elliott, S.J.

(2020) J Am Chem Soc 142: 11978-11982

  • DOI: https://doi.org/10.1021/jacs.0c04023
  • Primary Citation of Related Structures:  
    6V59

  • PubMed Abstract: 

    BthA is a diheme enzyme that is a member of the bacterial cytochrome c peroxidase superfamily, capable of generating a highly unusual Fe(IV)Fe(IV)═O oxidation state, known to be responsible for long-range oxidative chemistry in the enzyme MauG. Here, we show that installing a canonical Met ligand in lieu of the Tyr found at the heme of MauG associated with electron transfer, results in a construct that yields an unusually stable Fe(IV)═O porphyrin at the peroxidatic heme. This state is spontaneously formed at ambient conditions using either molecular O 2 or H 2 O 2 . The resulting data illustrate how a ferryl iron, with unforeseen stability, may be achieved in biology.


  • Organizational Affiliation

    Boston University, Department of Chemistry, Boston, Massachusetts 02215, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Di-haem cytochrome c peroxidase family protein
A, B
477Burkholderia thailandensis E264Mutation(s): 1 
Gene Names: BTH_II1092
UniProt
Find proteins for Q2T6B0 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264))
Explore Q2T6B0 
Go to UniProtKB:  Q2T6B0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2T6B0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth B],
M [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
N [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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I [auth A],
J [auth A],
U [auth B],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.97α = 90
b = 87.605β = 90
c = 184.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States008334

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description