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- PDB-8cng: Pa.FabF-C164Q in complex with ~{N}-cyclopentyl-3-methyl-1~{H}-pyr... -

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Basic information

Entry
Database: PDB / ID: 8cng
TitlePa.FabF-C164Q in complex with ~{N}-cyclopentyl-3-methyl-1~{H}-pyrazole-5-carboxamide
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / protein-ligand complex / FabF
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
Chem-V6L / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33210
Polymers86,6452
Non-polymers6868
Water8,179454
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-48 kcal/mol
Surface area24870 Å2
Unit cell
Length a, b, c (Å)65.737, 83.898, 137.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 3 - 412 / Label seq-ID: 2 - 411

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-V6L / ~{N}-cyclopentyl-3-methyl-1~{H}-pyrazole-5-carboxamide


Mass: 193.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
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: MAX IV / Beamline: BioMAX / Wavelength: 0.984002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984002 Å / Relative weight: 1
ReflectionResolution: 2.1→29.65 Å / Num. obs: 45179 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.983 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 12 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3638 / CC1/2: 0.75 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.67 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.156 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23086 2256 5 %RANDOM
Rwork0.18755 ---
obs0.18979 42852 99.88 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2---0.98 Å20 Å2
3---1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 39 454 6545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175878
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.6338404
X-RAY DIFFRACTIONr_angle_other_deg1.2981.57613481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9655826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3520.459327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41715980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4851559
X-RAY DIFFRACTIONr_chiral_restr0.0640.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
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_it2.2061.8123286
X-RAY DIFFRACTIONr_mcbond_other2.1991.8123285
X-RAY DIFFRACTIONr_mcangle_it2.9322.7114106
X-RAY DIFFRACTIONr_mcangle_other2.9322.7114107
X-RAY DIFFRACTIONr_scbond_it3.5542.3232934
X-RAY DIFFRACTIONr_scbond_other3.5532.3232935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1843.3064295
X-RAY DIFFRACTIONr_long_range_B_refined6.38823.2256936
X-RAY DIFFRACTIONr_long_range_B_other6.29522.9946854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12859 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 172 -
Rwork0.197 3094 -
obs--99.85 %

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