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- PDB-7oc1: Structure of Pseudomonas aeruginosa FabF mutant C164Q in complex ... -

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Basic information

Entry
Database: PDB / ID: 7oc1
TitleStructure of Pseudomonas aeruginosa FabF mutant C164Q in complex with Platensimycin
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsANTIBIOTIC / Inhibitor / Fatty acid biosynthesis pathway
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 / 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
: / PLATENSIMYCIN / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGeorgiou, C. / Brenk, R. / Espeland, L.O. / Klein, R.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
CitationJournal: Chemmedchem / Year: 2021
Title: An Experimental Toolbox for Structure-Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics.
Authors: Espeland, L.O. / Georgiou, C. / Klein, R. / Bhukya, H. / Haug, B.E. / Underhaug, J. / Mainkar, P.S. / Brenk, R.
History
DepositionApr 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)88,51917
Polymers86,6452
Non-polymers1,87415
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-42 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.024, 137.199, 65.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 43322.715 Da / Num. of mol.: 2 / Mutation: C164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: O54440, beta-ketoacyl-[acyl-carrier-protein] synthase II

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Non-polymers , 5 types, 447 molecules

#2: Chemical ChemComp-PMN / PLATENSIMYCIN


Mass: 441.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27NO7 / Comment: antibiotic*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.24M NH4HCO2 and 31.2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918399 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918399 Å / Relative weight: 1
ReflectionResolution: 1.8→68.69 Å / Num. obs: 71222 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.045 / Rrim(I) all: 0.118 / Net I/σ(I): 11.05
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.98 / Num. unique obs: 3493 / CC1/2: 0.952 / Rpim(I) all: 0.135 / Rrim(I) all: 0.352 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JB6

4jb6


Resolution: 1.8→68.69 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.977 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18773 3510 4.9 %RANDOM
Rwork0.15732 ---
obs0.15882 67633 99.92 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 115 432 6621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0176421
X-RAY DIFFRACTIONr_bond_other_d0.0010.0196092
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.8728721
X-RAY DIFFRACTIONr_angle_other_deg1.2112.65413988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2485862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39320.456329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.282151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9071560
X-RAY DIFFRACTIONr_chiral_restr0.0960.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021507
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_it1.4950.8373343
X-RAY DIFFRACTIONr_mcbond_other1.490.8363342
X-RAY DIFFRACTIONr_mcangle_it2.2431.2474189
X-RAY DIFFRACTIONr_mcangle_other2.2431.2484190
X-RAY DIFFRACTIONr_scbond_it2.921.1833078
X-RAY DIFFRACTIONr_scbond_other2.921.1843079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0261.6414516
X-RAY DIFFRACTIONr_long_range_B_refined4.90710.7677100
X-RAY DIFFRACTIONr_long_range_B_other4.8810.6767044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 232 -
Rwork0.154 4925 -
obs--99.02 %

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