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- PDB-8cne: Pa.FabF-C164A in complex with N-(propan-2-yl)-1H-pyrazole-3-carbo... -

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Basic information

Entry
Database: PDB / ID: 8cne
TitlePa.FabF-C164A in complex with N-(propan-2-yl)-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 / PHOSPHATE ION / N-(propan-2-yl)-1H-pyrazole-3-carboxamide / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGeorgiou, C. / Brenk, R. / Espeland, L.O.
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)89,29619
Polymers87,9932
Non-polymers1,30317
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint8 kcal/mol
Surface area30350 Å2
Unit cell
Length a, b, c (Å)101.202, 104.378, 142.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

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: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 413 / Label seq-ID: 8 - 418

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

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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, 257 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-Q5L / N-(propan-2-yl)-1H-pyrazole-3-carboxamide


Mass: 153.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
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: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.566→72.66 Å / Num. obs: 105352 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.3
Reflection shellResolution: 1.566→1.593 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5191 / CC1/2: 0.801 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→64.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.772 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20396 5151 4.9 %RANDOM
Rwork0.182 ---
obs0.18307 100075 99.64 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---0.22 Å2-0 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.57→64.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 77 240 6371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136312
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175980
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.6338530
X-RAY DIFFRACTIONr_angle_other_deg1.3691.57713712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40320.181332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97615990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1981562
X-RAY DIFFRACTIONr_chiral_restr0.0690.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021506
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_it2.3862.3243316
X-RAY DIFFRACTIONr_mcbond_other2.3872.3243317
X-RAY DIFFRACTIONr_mcangle_it3.2453.484150
X-RAY DIFFRACTIONr_mcangle_other3.2453.4814151
X-RAY DIFFRACTIONr_scbond_it3.922.892994
X-RAY DIFFRACTIONr_scbond_other3.9192.8922995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7674.1394371
X-RAY DIFFRACTIONr_long_range_B_refined6.66428.3866607
X-RAY DIFFRACTIONr_long_range_B_other6.65828.3436589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13011 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.57→1.607 Å
RfactorNum. reflection% reflection
Rfree0.277 387 -
Rwork0.275 7297 -
obs--99.42 %

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