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- PDB-8cou: Pa.FabF-C164Q in complex with 3-acetamido-4-methoxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 8cou
TitlePa.FabF-C164Q in complex with 3-acetamido-4-methoxybenzoic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / FabF / complex / pseudomonas aeruginosa
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 / 3-acetamido-4-methoxy-benzoic acid / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 28, 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)89,96738
Polymers86,9082
Non-polymers3,06036
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint7 kcal/mol
Surface area24390 Å2
Unit cell
Length a, b, c (Å)70.924, 64.631, 84.390
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211

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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: 43453.914 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

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Non-polymers , 5 types, 446 molecules

#2: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-VCZ / 3-acetamido-4-methoxy-benzoic acid


Mass: 209.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 42.49 %
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: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.68→80.99 Å / Num. obs: 82149 / % possible obs: 98.6 % / Redundancy: 2.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.117 / Net I/σ(I): 6.3
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4351 / CC1/2: 0.359 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→46.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.861 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19795 4248 5.2 %RANDOM
Rwork0.1738 ---
obs0.17508 77881 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.831 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20.36 Å2
2---0.68 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.68→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 166 410 6658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176130
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.638642
X-RAY DIFFRACTIONr_angle_other_deg1.481.57314024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1425849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5720.491326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69615996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6631559
X-RAY DIFFRACTIONr_chiral_restr0.080.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021494
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_it1.7062.3553330
X-RAY DIFFRACTIONr_mcbond_other1.7052.3533329
X-RAY DIFFRACTIONr_mcangle_it2.3163.5264168
X-RAY DIFFRACTIONr_mcangle_other2.3173.5284169
X-RAY DIFFRACTIONr_scbond_it2.9122.8133074
X-RAY DIFFRACTIONr_scbond_other2.9122.8143075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1974.0564464
X-RAY DIFFRACTIONr_long_range_B_refined5.2229.5087095
X-RAY DIFFRACTIONr_long_range_B_other5.18829.3127027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 309 -
Rwork0.3 5714 -
obs--98.05 %

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