7PPS | pdb_00007pps

apo FabB from Pseudomonas aeruginosa with single point mutation C161A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.137 (Depositor), 0.141 (DCC) 
  • R-Value Work: 
    0.114 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 
    0.115 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Crystal structure of Pseudomonas aeruginosa FabB C161A, a template for structure-based design for new antibiotics.

Yadrykhins'ky, V., Georgiou, C., Brenk, R.

(2021) F1000Res 10

  • DOI: https://doi.org/10.12688/f1000research.74018.2
  • Primary Citation Related Structures: 
    7PPS

  • PubMed Abstract: 

    Background : FabB (3-oxoacyl-[acyl-carrier-protein] synthase 1) is part of the fatty acid synthesis II pathway found in bacteria and a potential target for antibiotics. The enzyme catalyses the Claisen condensation of malonyl-ACP (acyl carrier protein) with acyl-ACP via an acyl-enzyme intermediate. Here, we report the crystal structure of the intermediate-mimicking Pseudomonas aeruginosa FabB ( Pa FabB) C161A variant. Methods : His-tagged Pa FabB C161A was expressed in E. coli Rosetta DE3 pLysS cells, cleaved by TEV protease and purified using affinity and size exclusion chromatography. Commercial screens were used to identify suitable crystallization conditions which were subsequently improved to obtain well diffracting crystals. Results : We developed a robust and efficient system for recombinant expression of Pa FabB C161A. Conditions to obtain well diffracting crystals were established. The crystal structure of Pa FabB C161A was solved by molecular replacement at 1.3 Å resolution. Binding site comparison between Pa FabB and Pa FabF revealed a conserved malonyl binding site but differences in the fatty acid binding channel. Conclusions : The Pa FabB C161A crystal structure can be used as a template to facilitate the design of FabB inhibitors.

    • Organizational Affiliation: 
    • Department of Biomedicine, University of Bergen, Bergen, 5020, Norway.

Macromolecule Content 

  • Total Structure Weight: 88.9 kDa 
  • Atom Count: 6,695 
  • Modeled Residue Count: 808 
  • Deposited Residue Count: 814 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 1
A, B
407Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 1 
Gene Names: fabB, PA14_43690
EC: 2.3.1.41
UniProt
Find proteins for Q02K94 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02K94 
Go to UniProtKB:  Q02K94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02K94
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD


Download:Ideal Coordinates CCD File
FA [auth B]
GA [auth B]
L [auth A]
M [auth A]
N [auth A]
FA [auth B],
GA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
U [auth A]
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
U [auth A],
V [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.137 (Depositor), 0.141 (DCC) 
  • R-Value Work:  0.114 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 0.115 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.228α = 90
b = 102.304β = 90
c = 188.774γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Council of NorwayNorway273588

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.2: 2022-02-16
    Changes: Database references
  • Version 1.3: 2022-02-23
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Database references, Refinement description