3OS6

Crystal structure of putative 2,3-dihydroxybenzoate-specific isochorismate synthase, DhbC from Bacillus anthracis.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of isochorismate synthase DhbC from Bacillus anthracis.

Domagalski, M.J., Tkaczuk, K.L., Chruszcz, M., Skarina, T., Onopriyenko, O., Cymborowski, M., Grabowski, M., Savchenko, A., Minor, W.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 956-961

  • DOI: 10.1107/S1744309113021246
  • Primary Citation of Related Structures:  
    3OS6

  • PubMed Abstract: 

    • The isochorismate synthase DhbC from Bacillus anthracis is essential for the biosynthesis of the siderophore bacillibactin by this pathogenic bacterium. The structure of the selenomethionine-substituted protein was determined to 2.4 Å resolution using single-wavelength anomalous diffraction ...

    The isochorismate synthase DhbC from Bacillus anthracis is essential for the biosynthesis of the siderophore bacillibactin by this pathogenic bacterium. The structure of the selenomethionine-substituted protein was determined to 2.4 Å resolution using single-wavelength anomalous diffraction. B. anthracis DhbC bears the strongest resemblance to the Escherichia coli isochorismate synthase EntC, which is involved in the biosynthesis of another siderophore, namely enterobactin. Both proteins adopt the characteristic fold of other chorismate-utilizing enzymes, which are involved in the biosynthesis of various products, including siderophores, menaquinone and tryptophan. The conservation of the active-site residues, as well as their spatial arrangement, suggests that these enzymes share a common Mg(2+)-dependent catalytic mechanism.

    Organizational Affiliation: 

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Charlottesville, VA 22908, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isochorismate synthase DhbCA, B, C, D399Bacillus anthracis str. AmesMutation(s): 0 
Gene Names: BAS2205, BA_2369, dhbC, GBAA2369, GBAA_2369
EC: 5.4.4.2
UniProt
Find proteins for A0A6H3A7J7 (Bacillus anthracis)
Explore A0A6H3A7J7 
Go to UniProtKB:  A0A6H3A7J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6H3A7J7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P
Download Ideal Coordinates CCD File 
M [auth A],
NA [auth D]		POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
E [auth A],
EA [auth D],
F [auth A],
AA [auth C],
BA [auth C],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
CA [auth C],
DA [auth C],
LA [auth D],
MA [auth D],
N [auth A],
CA [auth C],
DA [auth C],
LA [auth D],
MA [auth D],
N [auth A],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 3
  • Diffraction Data DOI: 10.18430/M3KK5Z
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.389α = 90
b = 201.389β = 90
c = 201.389γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-11
    Changes: Database references
  • Version 1.3: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary