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- PDB-8uix: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8uix
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, boronic acid-based compound Y43 bound
ComponentsFluorophosphonate-binding serine hydrolase E
KeywordsHYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / boronic acid / covalent / boron-serine / boron-histidine
Function / homologyHydrolases / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / membrane / : / Uncharacterized hydrolase SAUSA300_2518
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFellner, M.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat Commun / Year: 2025
Title: Identification of covalent inhibitors of Staphylococcus aureus serine hydrolases important for virulence and biofilm formation.
Authors: Upadhyay, T. / Woods, E.C. / Dela Ahator, S. / Julin, K. / Faucher, F.F. / Uddin, M.J. / Hollander, M.J. / Pedowitz, N.J. / Abegg, D. / Hammond, I. / Eke, I.E. / Wang, S. / Chen, S. / ...Authors: Upadhyay, T. / Woods, E.C. / Dela Ahator, S. / Julin, K. / Faucher, F.F. / Uddin, M.J. / Hollander, M.J. / Pedowitz, N.J. / Abegg, D. / Hammond, I. / Eke, I.E. / Wang, S. / Chen, S. / Bennett, J.M. / Jo, J. / Lentz, C.S. / Adibekian, A. / Fellner, M. / Bogyo, M.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorophosphonate-binding serine hydrolase E
B: Fluorophosphonate-binding serine hydrolase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9144
Polymers62,5502
Non-polymers3642
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-89 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.332, 47.001, 70.746
Angle α, β, γ (deg.)90.00, 96.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fluorophosphonate-binding serine hydrolase E


Mass: 31275.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: SAUSA300_2518 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-WS8 / (3,5-dimethoxyphenyl)boronic acid


Mass: 181.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11BO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20uL 25.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL Z27 (50mM in DMSO) and incubated at 4C overnight. 0.3 uL FphE-Z27 solution was mixed with 0.15 uL of reservoir ...Details: 20uL 25.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL Z27 (50mM in DMSO) and incubated at 4C overnight. 0.3 uL FphE-Z27 solution was mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180mM Calcium acetate, 100mM MES pH 6.5, 22.5% PEG 2000 MME. Crystal appeared within 2.5 days at 16C and grew until 14.5 days when it was frozen in a solution of ~25% glycerol, 75% reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.39→45.19 Å / Num. obs: 21675 / % possible obs: 99.6 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 0.99 / Net I/σ(I): 11.4 / Num. measured all: 147924
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 96.7 % / Redundancy: 7 % / Rmerge(I) obs: 1.17 / Num. measured all: 15162 / Num. unique obs: 2181 / CC1/2: 0.625 / Rpim(I) all: 0.475 / Rrim(I) all: 1.264 / Χ2: 1.03 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDS20220220data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→45.19 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 1066 4.92 %
Rwork0.1986 --
obs0.2022 21667 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4397 0 24 36 4457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094526
X-RAY DIFFRACTIONf_angle_d1.0356141
X-RAY DIFFRACTIONf_dihedral_angle_d8.37600
X-RAY DIFFRACTIONf_chiral_restr0.056665
X-RAY DIFFRACTIONf_plane_restr0.008807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.50.38821190.30672498X-RAY DIFFRACTION97
2.5-2.630.32291270.2822559X-RAY DIFFRACTION100
2.63-2.790.35431280.2682562X-RAY DIFFRACTION100
2.8-3.010.30921350.25392562X-RAY DIFFRACTION100
3.01-3.310.32881340.24282572X-RAY DIFFRACTION100
3.31-3.790.29441270.21022585X-RAY DIFFRACTION100
3.79-4.780.23561580.16462597X-RAY DIFFRACTION100
4.78-45.190.22961380.15832666X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1702-1.5761-0.30322.50081.27262.4713-0.11240.01970.2161-0.07870.4137-0.8046-0.74141.5168-0.28680.5052-0.07510.15450.7197-0.06820.7242-10.7297-11.574614.183
27.03671.3995-0.86223.3982-0.71954.2879-0.0013-0.01990.39090.00770.1874-0.1889-0.6315-0.0759-0.17240.47830.0863-0.02310.32070.01840.3191-25.4381-8.34915.0186
33.8811.33851.9292.97240.15124.06490.4506-0.847-0.35310.2793-0.1266-0.1120.4195-0.6236-0.29170.4616-0.1106-0.04690.4780.09470.514-24.8695-37.546249.1517
46.2651.58292.90595.57952.27585.73710.3265-0.47440.02620.01-0.1785-0.52470.08160.0494-0.11010.2725-0.0351-0.00320.33440.06790.4883-13.0562-29.517450.1843
50.8655-1.16412.06712.4872-2.32545.11-0.02960.083-0.3112-0.17270.3220.11340.4984-0.5045-0.25160.5518-0.06080.08360.493-0.05940.6204-32.6051-32.556321.8093
66.50041.7141-0.91882.9294-0.05124.6467-0.28060.0106-0.0154-0.17940.3184-0.1821-0.543-0.6267-0.02480.42240.12760.01270.46050.02360.3439-33.8029-10.490514.7312
75.93640.6339-1.53272.1157-0.75793.4698-0.22092.3787-0.0213-1.43730.1830.1554-0.0562-0.781-0.02970.7534-0.01910.02810.9610.05670.3985-30.6293-11.4833-0.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 183 )
6X-RAY DIFFRACTION6chain 'B' and (resid 184 through 246 )
7X-RAY DIFFRACTION7chain 'B' and (resid 247 through 276 )

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