3OS6 | pdb_00003os6

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

PDB DOI: https://doi.org/10.2210/pdb3OS6/pdb

Classification: ISOMERASE
Organism(s): Bacillus anthracis str. Ames
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-08 Released: 2010-10-20
Deposition Author(s): Domagalski, M.J., Chruszcz, M., Skarina, T., Onopriyenko, O., Cymborowski, M., Savchenko, A., Edwards, A., Anderson, W., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.212 (Depositor), 0.222 (DCC)
R-Value Work:
0.171 (Depositor), 0.187 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 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

PubMed: 23989140 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113021246
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 186.28 kDa
Atom Count: 12,607
Modeled Residue Count: 1,495
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isochorismate synthase DhbC	A, B, C, D	399	Bacillus anthracis str. Ames	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6H3A7J7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain NA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D]	M [auth A], NA [auth D]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain NA [auth D] Interactions & Density Focus chain M [auth A] Focus chain NA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain HA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain HA [auth D]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain DA [auth C]	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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain N [auth A] Focus chain V [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.212 (Depositor), 0.222 (DCC)
R-Value Work: 0.171 (Depositor), 0.187 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.389	α = 90
b = 201.389	β = 90
c = 201.389	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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
Version 1.4: 2024-11-06
Changes: Data collection, Structure summary