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- PDB-8cn8: apo Pseudomonas aeruginosa FabF C164A mutant -

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Basic information

Entry
Database: PDB / ID: 8cn8
Titleapo Pseudomonas aeruginosa FabF C164A mutant
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / FabF / complex / platencin / antibiotic
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeorgiou, C. / Brenk, R. / Espeland, L.O.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
Citation
Journal: Eur.J.Med.Chem. / Year: 2025
Title: Towards new antibiotics: P. aeruginosa FabF ligands discovered by crystallographic fragment screening followed by hit expansion.
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhins'ky, V. / Haug, B.E. / Mainkar, P.S. / Brenk, R.
#1: Journal: Chemrxiv / Year: 2023
Title: New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R.
History
DepositionFeb 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 2
D: 3-oxoacyl-[acyl-carrier-protein] synthase 2


Theoretical massNumber of molelcules
Total (without water)175,9864
Polymers175,9864
Non-polymers00
Water23,3291295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-108 kcal/mol
Surface area50190 Å2
Unit cell
Length a, b, c (Å)70.837, 72.496, 139.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43996.496 Da / Num. of mol.: 4 / Mutation: C164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1295 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.20M ammonium formate and 31.2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.976246 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.8→47.63 Å / Num. obs: 126727 / % possible obs: 96.8 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 6098 / CC1/2: 0.949 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.141 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17474 6629 5.2 %RANDOM
Rwork0.14132 ---
obs0.14309 120077 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.797 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.11 Å2
2---0.38 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12312 0 0 1295 13607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312828
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712137
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.63217407
X-RAY DIFFRACTIONr_angle_other_deg1.5171.57527905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09651756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21420.329668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.794152049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21215123
X-RAY DIFFRACTIONr_chiral_restr0.0880.21665
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023041
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5891.7496793
X-RAY DIFFRACTIONr_mcbond_other1.5891.7496792
X-RAY DIFFRACTIONr_mcangle_it2.2662.6178512
X-RAY DIFFRACTIONr_mcangle_other2.2662.6178513
X-RAY DIFFRACTIONr_scbond_it2.6612.1356035
X-RAY DIFFRACTIONr_scbond_other2.6612.1356033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1633.0658857
X-RAY DIFFRACTIONr_long_range_B_refined5.37722.34714592
X-RAY DIFFRACTIONr_long_range_B_other5.27521.9114266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 428 -
Rwork0.157 8813 -
obs--95.84 %

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