5A12

Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with azide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Ligand Binding to Chlorite Dismutase from Magnetospirillum Sp.

De Schutter, A., Correia, H., Freire, D.M., Rivas, M.G., Rizzi, A.C., Santos-Silva, T., Gonzalez, P.J., Van Doorslaer, S.

(2015) J Phys Chem B 119: 13859

  • DOI: 10.1021/acs.jpcb.5b04141
  • Primary Citation of Related Structures:  
    5A12, 5A13

  • PubMed Abstract: 

    • Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms ...

    Chlorite dismutase (Cld) catalyzes the reduction of chlorite to chloride and dioxygen. Here, the ligand binding to Cld of Magnetospirillum sp. (MaCld) is investigated with X-ray crystallography and electron paramagnetic resonance (EPR). EPR reveals a large heterogeneity in the structure of wild-type MaCld, showing a variety of low- and high-spin ferric heme forms. Addition of an axial ligand, such as azide or imidazole, removes this heterogeneity almost entirely. This is in line with the two high resolution crystal structures of MaCld obtained in the presence of azide and thiocyanate that show the coordination of the ligands to the heme iron. The crystal structure of the MaCld-azide complex reveals a single well-defined orientation of the azide molecule in the heme pocket. EPR shows, however, a pH-dependent heme structure, probably due to acid-base transitions of the surrounding amino-acid residues stabilizing azide. For the azide and imidazole complex of MaCld, the hyperfine and nuclear quadrupole interactions with the close-by (14)N and (1)H nuclei are determined using pulsed EPR. These values are compared to the corresponding data for the low-spin forms observed in the ferric wild-type MaCld and to existing EPR data on azide and imidazole complexes of other heme proteins.

    Organizational Affiliation: 

    BIMEF Laboratory, Department of Physics, University of Antwerp , Universiteitsplein 1, B-2610 Wilrijk, Belgium.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHLORITE DISMUTASEA, B, C, D, E242Magnetospirillum sp.Mutation(s): 0 
EC: 1.13.11.49
UniProt
Find proteins for A0A0M3KL46 (Magnetospirillum sp)
Explore A0A0M3KL46 
Go to UniProtKB:  A0A0M3KL46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL46
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
P [auth D],
T [auth E]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
H [auth A],
K [auth B],
N [auth C],
O [auth C],
R [auth D],
S [auth D],
V [auth E],
W [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
AZI
Query on AZI
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
Q [auth D],
U [auth E]		AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.234α = 90
b = 133.823β = 113.03
c = 77.622γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references
  • Version 1.2: 2017-03-22
    Changes: Data collection