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- PDB-8cn5: Pa.FabF-C164Q in complex with propan-2-yl 1~{H}-pyrazole-3-carboxylate -

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Basic information

Entry
Database: PDB / ID: 8cn5
TitlePa.FabF-C164Q in complex with propan-2-yl 1~{H}-pyrazole-3-carboxylate
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / FabF / complex
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
PHOSPHATE ION / propan-2-yl 1~{H}-pyrazole-3-carboxylate / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGeorgiou, C. / Brenk, R.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
CitationJournal: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,00230
Polymers86,6452
Non-polymers2,35728
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-17 kcal/mol
Surface area25500 Å2
Unit cell
Length a, b, c (Å)71.752, 65.705, 84.861
Angle α, β, γ (deg.)90.00, 102.11, 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: 43322.715 Da / Num. of mol.: 2 / Mutation: C164Q
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: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-V5K / propan-2-yl 1~{H}-pyrazole-3-carboxylate


Mass: 154.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.51 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.932→51.511 Å / Num. obs: 57577 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.977 / Rmerge(I) obs: 0.154 / Net I/σ(I): 6
Reflection shellResolution: 1.932→1.965 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / Num. unique obs: 2807 / CC1/2: 0.806 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→51.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.708 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2812 4.9 %RANDOM
Rwork0.16569 ---
obs0.16765 54761 99.21 %-
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: 28.224 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20.64 Å2
2--0.79 Å20 Å2
3----2.36 Å2
Refinement stepCycle: 1 / Resolution: 1.93→51.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 127 432 6633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156089
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6328608
X-RAY DIFFRACTIONr_angle_other_deg1.3691.57413946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9995850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0820.52327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0771559
X-RAY DIFFRACTIONr_chiral_restr0.0770.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021491
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_it1.962.7193328
X-RAY DIFFRACTIONr_mcbond_other1.962.7183327
X-RAY DIFFRACTIONr_mcangle_it2.6724.0694166
X-RAY DIFFRACTIONr_mcangle_other2.6724.074167
X-RAY DIFFRACTIONr_scbond_it2.9613.1853044
X-RAY DIFFRACTIONr_scbond_other2.963.1843045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3654.614431
X-RAY DIFFRACTIONr_long_range_B_refined5.56433.3356794
X-RAY DIFFRACTIONr_long_range_B_other5.54133.1466736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 220 -
Rwork0.229 4020 -
obs--99.37 %

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