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- PDB-9i7k: Pseudomonas aeruginosa FabF C164A in complex with N-(3-(2-(1H-pyr... -

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Basic information

Entry
Database: PDB / ID: 9i7k
TitlePseudomonas aeruginosa FabF C164A in complex with N-(3-(2-(1H-pyrrol-1-yl)propanamido)-2-hydroxy-2-methylpropyl)-1H-pyrazole-3-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
: / FORMIC ACID / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.827 Å
AuthorsYadrykhinsky, V. / Brenk, R.
Funding support Norway, 2items
OrganizationGrant numberCountry
Other governmentF12602
Research Council of Norway273588 Norway
CitationJournal: 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.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: 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)90,15321
Polymers87,9932
Non-polymers2,16019
Water3,981221
1
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)89,95118
Polymers87,9932
Non-polymers1,95816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area9620 Å2
ΔGint-47 kcal/mol
Surface area24960 Å2
2
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)90,35624
Polymers87,9932
Non-polymers2,36322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11500 Å2
ΔGint-35 kcal/mol
Surface area24360 Å2
Unit cell
Length a, b, c (Å)100.744, 104.195, 142.593
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 4 - 412 / Label seq-ID: 9 - 417

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 43996.496 Da / Num. of mol.: 2
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-A1I03 / ~{N}-[(2~{S})-2-methyl-2-oxidanyl-3-[[(2~{S})-2-pyrrol-1-ylpropanoyl]amino]propyl]-1~{H}-pyrazole-3-carboxamide


Mass: 319.359 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.24 ammonium formate and 35% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873129 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873129 Å / Relative weight: 1
ReflectionResolution: 1.827→72.426 Å / Num. obs: 66594 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.99 / Net I/σ(I): 5.8
Reflection shellResolution: 1.827→1.858 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3321 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROC1.1.7data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.827→72.426 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.173 / SU B: 8.07 / SU ML: 0.111 / Average fsc free: 0.9581 / Average fsc work: 0.9693 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2172 3267 4.934 %
Rwork0.1731 62949 -
all0.175 --
obs-66216 99.394 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.701 Å2
Baniso -1Baniso -2Baniso -3
1--1.666 Å2-0 Å20 Å2
2--0.327 Å2-0 Å2
3---1.339 Å2
Refinement stepCycle: LAST / Resolution: 1.827→72.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 117 221 6381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126277
X-RAY DIFFRACTIONr_bond_other_d0.0050.0165910
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.8028485
X-RAY DIFFRACTIONr_angle_other_deg1.0411.73413522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.0415.96862
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg9.80554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85310954
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.93810256
X-RAY DIFFRACTIONr_chiral_restr0.1230.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027704
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021486
X-RAY DIFFRACTIONr_nbd_refined0.1870.21151
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1390.25361
X-RAY DIFFRACTIONr_nbtor_refined0.1540.23074
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.23455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.219
X-RAY DIFFRACTIONr_nbd_other0.0880.2238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0890.225
X-RAY DIFFRACTIONr_mcbond_it2.0251.7373313
X-RAY DIFFRACTIONr_mcbond_other2.0251.7373314
X-RAY DIFFRACTIONr_mcangle_it2.7513.1214147
X-RAY DIFFRACTIONr_mcangle_other2.7513.1224148
X-RAY DIFFRACTIONr_scbond_it4.0232.3252964
X-RAY DIFFRACTIONr_scbond_other4.0222.3252965
X-RAY DIFFRACTIONr_scangle_it5.9694.0344330
X-RAY DIFFRACTIONr_scangle_other5.9694.0344331
X-RAY DIFFRACTIONr_lrange_it6.75817.9486673
X-RAY DIFFRACTIONr_lrange_other6.75817.9366656
X-RAY DIFFRACTIONr_ncsr_local_group_10.0680.0512892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.06780.05008
12BX-RAY DIFFRACTIONLocal ncs0.06780.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.827-1.8740.3092230.32243890.32148640.9150.90994.81910.322
1.874-1.9250.3082480.29144250.29247520.9160.9398.33750.29
1.925-1.9810.2922280.26643720.26746240.9320.94499.4810.263
1.981-2.0420.2842200.24142660.24344930.9420.95499.84420.233
2.042-2.1090.2362310.20541310.20643680.9570.96999.86260.195
2.109-2.1830.2392310.19139830.19342190.9630.97599.88150.179
2.183-2.2650.232010.17738930.17940960.9650.97899.95120.164
2.265-2.3580.2481610.16337280.16738930.9590.98299.89730.151
2.358-2.4630.1951840.15436000.15637860.9740.98699.94720.141
2.463-2.5830.2181930.14834160.15236090.970.9861000.137
2.583-2.7220.1961680.14632590.14934290.9740.98799.94170.137
2.722-2.8870.1981420.1531220.15232660.9750.98699.93880.144
2.887-3.0860.2071660.1528870.15330530.9730.9851000.146
3.086-3.3330.1771380.14327400.14428780.9810.9871000.145
3.333-3.650.2031310.15125000.15426320.9760.98699.9620.161
3.65-4.080.1841270.14522790.14724070.980.98999.95850.162
4.08-4.7080.179930.13520470.13721400.9870.991000.16
4.708-5.760.183840.15717260.15918100.9820.9881000.19
5.76-8.120.231580.16713850.1714430.9710.9841000.203
8.12-72.4260.193400.188010.1818470.9710.9899.29160.238
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7851-0.09990.31140.06180.00770.1692-0.0148-0.0382-0.059-0.0230.00290.0406-0.0317-0.0210.0120.01390.0083-0.01520.05950.00530.027535.87623.6527-39.2033
20.27260.06760.00720.3108-0.25850.2581-0.01420.01480.06760.02070.02630.0342-0.00910.014-0.01210.02360.00280.00020.0504-0.00170.02055.355614.3672-3.482
Refinement TLS groupSelection: ALL

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