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- PDB-9i76: Pseudomonas aeruginosa FabF C164A in complex with 4-(1H-pyrazole-... -

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Basic information

Entry
Database: PDB / ID: 9i76
TitlePseudomonas aeruginosa FabF C164A in complex with 4-(1H-pyrazole-3-carboxamido)butanoic acid
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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / PHOSPHATE ION / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsYadrykhins'ky, V. / Brenk, R.
Funding support Norway, 1items
OrganizationGrant numberCountry
Other governmentF12602 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
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)90,18734
Polymers87,9932
Non-polymers2,19432
Water5,801322
1
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)89,50124
Polymers87,9932
Non-polymers1,50822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9730 Å2
ΔGint-54 kcal/mol
Surface area26330 Å2
MethodPISA
2
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)90,87444
Polymers87,9932
Non-polymers2,88142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9630 Å2
ΔGint-45 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.8, 103.8, 141.72
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 413 / Label seq-ID: 7 - 418

Dom-ID
1
2

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

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 43996.496 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-A1I0O / 4-(1~{H}-pyrazol-3-ylcarbonylamino)butanoic acid


Mass: 197.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.71 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.47→48.74 Å / Num. obs: 125625 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 13.2
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 7.3 % / Num. unique obs: 6169 / CC1/2: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
pointless1.12.8data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→48.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.383 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1898 6418 5.111 %
Rwork0.1616 119162 -
all0.163 --
obs-125580 99.811 %
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: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2--0.283 Å2-0 Å2
3---0.708 Å2
Refinement stepCycle: LAST / Resolution: 1.47→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 132 322 6520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126436
X-RAY DIFFRACTIONr_bond_other_d0.0030.0166128
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.8088691
X-RAY DIFFRACTIONr_angle_other_deg0.7911.74214029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.874569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.151101013
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.70910273
X-RAY DIFFRACTIONr_chiral_restr0.1090.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027938
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021548
X-RAY DIFFRACTIONr_nbd_refined0.2080.21214
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.25572
X-RAY DIFFRACTIONr_nbtor_refined0.170.23153
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23549
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2279
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0890.235
X-RAY DIFFRACTIONr_nbd_other0.140.2226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.223
X-RAY DIFFRACTIONr_mcbond_it2.3562.1053346
X-RAY DIFFRACTIONr_mcbond_other2.3592.1053347
X-RAY DIFFRACTIONr_mcangle_it3.2533.7784193
X-RAY DIFFRACTIONr_mcangle_other3.2533.784194
X-RAY DIFFRACTIONr_scbond_it4.4992.7093090
X-RAY DIFFRACTIONr_scbond_other4.4472.6933071
X-RAY DIFFRACTIONr_scangle_it6.2554.6994477
X-RAY DIFFRACTIONr_scangle_other6.2574.74478
X-RAY DIFFRACTIONr_lrange_it7.03122.1426899
X-RAY DIFFRACTIONr_lrange_other7.03422.1416898
X-RAY DIFFRACTIONr_ncsr_local_group_10.0670.0513317
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.067140.05009
12AX-RAY DIFFRACTIONLocal ncs0.067140.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.5080.4184430.4028796X-RAY DIFFRACTION99.7948
1.508-1.550.3484140.3398561X-RAY DIFFRACTION99.9777
1.55-1.5940.3134080.2868323X-RAY DIFFRACTION99.9885
1.594-1.6430.2454420.2438091X-RAY DIFFRACTION100
1.643-1.6970.244340.2217749X-RAY DIFFRACTION99.9633
1.697-1.7570.2354460.2037498X-RAY DIFFRACTION99.1389
1.757-1.8230.2094020.1767239X-RAY DIFFRACTION99.57
1.823-1.8970.183840.1527041X-RAY DIFFRACTION99.9731
1.897-1.9820.1774020.1456700X-RAY DIFFRACTION99.9859
1.982-2.0780.1783440.146488X-RAY DIFFRACTION100
2.078-2.190.173250.1346190X-RAY DIFFRACTION99.954
2.19-2.3230.1583000.1325831X-RAY DIFFRACTION99.9185
2.323-2.4830.1853150.1365435X-RAY DIFFRACTION99.4122
2.483-2.6810.1852720.1395141X-RAY DIFFRACTION100
2.681-2.9360.1842770.1454693X-RAY DIFFRACTION99.9799
2.936-3.2810.182270.1584306X-RAY DIFFRACTION99.9559
3.281-3.7860.1752140.1523795X-RAY DIFFRACTION99.9003
3.786-4.630.1531650.1373233X-RAY DIFFRACTION99.6481
4.63-6.5180.1981370.1712554X-RAY DIFFRACTION99.7775
6.518-48.730.209670.1811498X-RAY DIFFRACTION99.6181
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)
10.23140.07350.08550.29220.17540.15590.0137-0.0042-0.05850.01320.015-0.0290.0022-0.0247-0.02860.0103-0.003-0.00660.03490.00570.0169-5.0126-14.3522-3.1514
20.5126-0.0905-0.13210.0378-0.00970.0847-0.0168-0.02010.0556-0.0091-0.0049-0.03140.02440.02630.02170.00820.00880.01010.03720.00550.0289-36.1014-4.0877-38.7055
Refinement TLS groupSelection: ALL

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