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- PDB-8qer: Pseudomonas aeruginosa FabF C164A in complex with 4-(1H-pyrazole-... -

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Basic information

Entry
Database: PDB / ID: 8qer
TitlePseudomonas aeruginosa FabF C164A in complex with 4-(1H-pyrazole-3-carbonylamino)pentanoic 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 / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
FORMIC ACID / Chem-UGL / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYadrykhins'ky, V. / Brenk, R. / Georgiou, C.
Funding support Norway, 2items
OrganizationGrant numberCountry
Other governmentF-12602/4800005968
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
DepositionSep 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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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)89,47024
Polymers87,9932
Non-polymers1,47722
Water3,693205
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules

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


  • defined by author&software
  • Evidence: Software determined: Baum, Bernhard, et al. "Structures of Pseudomonas aeruginosa beta-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for ...Evidence: Software determined: Baum, Bernhard, et al. "Structures of Pseudomonas aeruginosa beta-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form." Acta Crystallographica Section F: Structural Biology Communications 71.8 (2015): 1020-1026.
  • 89.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)89,48226
Polymers87,9932
Non-polymers1,48924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8630 Å2
ΔGint-82 kcal/mol
Surface area25570 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)89,45822
Polymers87,9932
Non-polymers1,46520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area9190 Å2
ΔGint-74 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.322, 103.969, 140.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 411 / Label seq-ID: 6 - 416

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 , 6 types, 227 molecules

#2: Chemical ChemComp-UGL / (4~{R})-4-(1~{H}-pyrazol-3-ylcarbonylamino)pentanoic acid


Mass: 211.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.24M 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: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.95→48.764 Å / Num. obs: 53820 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.996 / Net I/σ(I): 8.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.3 % / Num. unique obs: 5219 / CC1/2: 0.555 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSJan 10, 2022data reduction
Aimless0.7.7 : 23/04/21data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.764 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.625 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2459 2690 5.002 %
Rwork0.1863 51093 -
all0.189 --
obs-53783 99.892 %
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: 38.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.329 Å2-0 Å20 Å2
2--0.13 Å2-0 Å2
3---2.199 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 88 205 6376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126293
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165922
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6388483
X-RAY DIFFRACTIONr_angle_other_deg0.6671.56913580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.4115.31763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0310981
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.95110267
X-RAY DIFFRACTIONr_chiral_restr0.0880.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027692
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021498
X-RAY DIFFRACTIONr_nbd_refined0.1970.21224
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.25515
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23119
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.234
X-RAY DIFFRACTIONr_nbd_other0.1090.2253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.228
X-RAY DIFFRACTIONr_mcbond_it3.4193.1973310
X-RAY DIFFRACTIONr_mcbond_other3.4193.1983311
X-RAY DIFFRACTIONr_mcangle_it4.3185.7384136
X-RAY DIFFRACTIONr_mcangle_other4.3185.7394137
X-RAY DIFFRACTIONr_scbond_it4.4283.7262983
X-RAY DIFFRACTIONr_scbond_other4.4273.7282984
X-RAY DIFFRACTIONr_scangle_it6.0126.6074343
X-RAY DIFFRACTIONr_scangle_other6.0126.6094344
X-RAY DIFFRACTIONr_lrange_it7.03332.1616795
X-RAY DIFFRACTIONr_lrange_other7.01232.0116768
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.0512930
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076460.05008
12AX-RAY DIFFRACTIONLocal ncs0.076460.05008
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
1.95-20.3292120.31937270.31939480.9090.91299.7720.317
2-2.0550.3072210.335750.337970.9050.92199.97370.294
2.055-2.1150.2921920.25835430.2637380.9270.94199.91970.25
2.115-2.180.2731620.24434610.24636270.9420.9599.88970.231
2.18-2.2510.2731720.21533440.21835160.9410.9631000.2
2.251-2.330.2861700.20132410.20534110.9430.9691000.184
2.33-2.4180.2351640.18331270.18532910.9610.9751000.164
2.418-2.5160.2351740.16429920.16831660.9610.981000.145
2.516-2.6280.2581620.17228610.17630240.9570.9899.96690.152
2.628-2.7550.2541280.17127920.17429200.9510.9811000.152
2.755-2.9040.2271210.1526650.15427860.9680.9861000.136
2.904-3.0790.2181550.15324750.15726330.9710.98699.88610.139
3.079-3.2910.2021210.14623660.14824870.9750.9861000.136
3.291-3.5530.232870.15622220.15923090.9590.9841000.153
3.553-3.8910.1961030.15920380.1621430.9720.98699.90670.158
3.891-4.3460.193860.16218560.16419440.980.98599.89710.168
4.346-5.0120.271800.16516580.1717400.9570.98299.88510.178
5.012-6.1220.214770.19213900.19314750.9750.9899.45760.206
6.122-8.5910.255580.21411020.21611630.9590.97399.74210.241
8.591-48.7640.401450.2856580.2917050.9130.94399.71630.346
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)
10.6449-0.1239-0.39370.07210.02370.30880-0.04790.1041-0.0273-0.0171-0.07510.04490.05680.0170.0260.01340.04470.02860.02050.0986-35.7055-4.185532.0189
20.20130.04360.05150.35210.24760.2225-0.01570.0039-0.08640.0410.0176-0.03770.0093-0.0198-0.00180.0496-0.00170.00030.0232-0.0210.0559-5.2616-14.518367.6031
Refinement TLS groupSelection: ALL

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