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- PDB-8r0i: Pseudomonas aeruginosa FabF C164A in complex with 3-amino-N-(1,5-... -

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Basic information

Entry
Database: PDB / ID: 8r0i
TitlePseudomonas aeruginosa FabF C164A in complex with 3-amino-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)benzamide
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 / 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 / : / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsYadrykhinsky, V. / Brenk, R.
Funding support Norway, 2items
OrganizationGrant numberCountry
Other governmentF-12602/4800005968
Research Council of Norway273588 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
DepositionOct 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,05412
Polymers87,9932
Non-polymers1,06110
Water5,044280
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)88,94610
Polymers87,9932
Non-polymers9538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7150 Å2
ΔGint-47 kcal/mol
Surface area24960 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)89,16214
Polymers87,9932
Non-polymers1,16912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6780 Å2
ΔGint-51 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.018, 103.667, 141.315
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-751-

HOH

21B-720-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 412 / Label seq-ID: 8 - 417

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 , 5 types, 290 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-XG7 / 3-azanyl-N-(1,5-dimethyl-3-oxidanylidene-2-phenyl-pyrazol-4-yl)benzamide / 3-amino-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)benzamide


Mass: 322.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.1 Å3/Da / Density % sol: 41.59 %
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: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.51→72.35 Å / Num. obs: 115834 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 5.9 % / Num. unique obs: 5652 / CC1/2: 0.293 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia23.12.0data reduction
DIALS3.12.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→72.349 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.186 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.236 5757 4.972 %
Rwork0.1916 110032 -
all0.194 --
obs-115789 99.895 %
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: 30.804 Å2
Baniso -1Baniso -2Baniso -3
1--1.471 Å2-0 Å20 Å2
2--0.62 Å2-0 Å2
3---0.851 Å2
Refinement stepCycle: LAST / Resolution: 1.51→72.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 74 280 6414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126328
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165959
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.6418558
X-RAY DIFFRACTIONr_angle_other_deg0.7341.5713665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.619569
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.02452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6510992
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.24210269
X-RAY DIFFRACTIONr_chiral_restr0.1050.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027796
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021528
X-RAY DIFFRACTIONr_nbd_refined0.2080.21254
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.25617
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23136
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.230
X-RAY DIFFRACTIONr_nbd_other0.1270.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.234
X-RAY DIFFRACTIONr_mcbond_it3.7232.9333321
X-RAY DIFFRACTIONr_mcbond_other3.7242.9333322
X-RAY DIFFRACTIONr_mcangle_it4.4765.2584157
X-RAY DIFFRACTIONr_mcangle_other4.4765.2594158
X-RAY DIFFRACTIONr_scbond_it4.7643.4573007
X-RAY DIFFRACTIONr_scbond_other4.7633.4583008
X-RAY DIFFRACTIONr_scangle_it6.576.1254393
X-RAY DIFFRACTIONr_scangle_other6.5696.1254394
X-RAY DIFFRACTIONr_lrange_it7.20628.8726948
X-RAY DIFFRACTIONr_lrange_other7.20828.7346912
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.0513148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.065670.05008
12AX-RAY DIFFRACTIONLocal ncs0.065670.05008
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
1.51-1.5490.3753650.38779910.38684430.8870.88298.96960.391
1.549-1.5920.3834160.36978860.3783020.8750.8811000.372
1.592-1.6380.3653460.36177160.36180620.8190.8141000.362
1.638-1.6880.3623800.34874820.34978620.8790.8931000.347
1.688-1.7440.343830.32871770.32975600.90.9091000.325
1.744-1.8050.2873660.29770280.29673940.9310.9281000.288
1.805-1.8730.3193620.27567000.27770620.930.9431000.261
1.873-1.9490.2583620.23264740.23368360.950.9611000.209
1.949-2.0360.2593190.20962570.21165760.9560.9691000.183
2.036-2.1350.2383580.18359290.18662870.9620.9771000.158
2.135-2.250.2412920.17957000.18259920.9640.9791000.155
2.25-2.3870.2293060.1753270.17356330.9680.9821000.144
2.387-2.5510.2212520.1650960.16353480.970.9841000.135
2.551-2.7560.2192700.15847020.16149720.9710.9851000.135
2.756-3.0180.2342340.16343810.16746150.9640.9831000.145
3.018-3.3740.2262190.17139430.17441620.9690.9821000.158
3.374-3.8940.2041500.15935520.1637020.9760.9861000.154
3.894-4.7660.181940.13429540.13731480.9820.9891000.137
4.766-6.7250.2051130.17223690.17424820.9810.9861000.173
6.725-72.3490.267700.22413680.22614390.9520.96799.93050.25

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