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- PDB-8pj0: Pseudomonas aeruginosa FabF C164A mutant in complex with N-(1,5-d... -

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Basic information

Entry
Database: PDB / ID: 8pj0
TitlePseudomonas aeruginosa FabF C164A mutant in complex with N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-3-methylbutanamide
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 / : / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGeorgiou, C. / Brenk, R. / Espeland, L.O.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway Norway
CitationJournal: Rsc Med Chem / Year: 2024
Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection.
Authors: Jalencas, X. / Berg, H. / Espeland, L.O. / Sreeramulu, S. / Kinnen, F. / Richter, C. / Georgiou, C. / Yadrykhinsky, V. / Specker, E. / Jaudzems, K. / Miletic, T. / Harmel, R. / Gribbon, P. / ...Authors: Jalencas, X. / Berg, H. / Espeland, L.O. / Sreeramulu, S. / Kinnen, F. / Richter, C. / Georgiou, C. / Yadrykhinsky, V. / Specker, E. / Jaudzems, K. / Miletic, T. / Harmel, R. / Gribbon, P. / Schwalbe, H. / Brenk, R. / Jirgensons, A. / Zaliani, A. / Mestres, J.
History
DepositionJun 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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


Theoretical massNumber of molelcules
Total (without water)177,74254
Polymers173,0634
Non-polymers4,67950
Water14,214789
1
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)88,55823
Polymers86,5312
Non-polymers2,02721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 2
D: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,18431
Polymers86,5312
Non-polymers2,65229
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.461, 141.345, 72.484
Angle α, β, γ (deg.)90, 91.64, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43265.664 Da / Num. of mol.: 4
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
#2: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CH2O2
#4: Chemical
ChemComp-ZHX / ~{N}-(1,5-dimethyl-3-oxidanylidene-2-phenyl-pyrazol-4-yl)-3-methyl-butanamide


Mass: 287.357 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 278 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: PETRA III, DESY / Beamline: P11 / Wavelength: 0.976246 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.7→48.83 Å / Num. obs: 158061 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.8 % / Num. unique obs: 7870 / CC1/2: 0.99 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.83 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.182 --RANDOM
Rwork0.162 ---
obs-150193 98.98 %-
Refinement stepCycle: LAST / Resolution: 1.7→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12136 0 266 789 13191

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