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

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Basic information

Entry
Database: PDB / ID: 8tfw
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, boronic acid-based compound N34 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: 1.93 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
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 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

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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)62,9665
Polymers62,5502
Non-polymers4163
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-94 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.972, 76.419, 73.380
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-ZKR / [5-(trifluoromethyl)thiophen-2-yl]boronic acid


Mass: 195.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4BF3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13uL 19 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL N34 (50mM in DMSO) and incubated at 18C overnight. 0.15 ul FphE-N34 solution was mixed with 0.3 ul of reservoir ...Details: 13uL 19 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL N34 (50mM in DMSO) and incubated at 18C overnight. 0.15 ul FphE-N34 solution was mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 0.18 M Magnesium chloride, 0.1 M MES pH 6.5, 22.5 % w/v Polyethylene glycol monomethyl ether 2000. Crystal 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: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→46.97 Å / Num. obs: 38831 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.065 / Rrim(I) all: 0.15 / Χ2: 0.99 / Net I/σ(I): 9 / Num. measured all: 199549
Reflection shellResolution: 1.93→1.97 Å / % possible obs: 98.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 1.195 / Num. measured all: 13197 / Num. unique obs: 2582 / CC1/2: 0.65 / Rpim(I) all: 0.566 / Rrim(I) all: 1.327 / Χ2: 0.93 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→40.01 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1882 4.87 %
Rwork0.2127 --
obs0.215 38663 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 23 147 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094528
X-RAY DIFFRACTIONf_angle_d1.0556151
X-RAY DIFFRACTIONf_dihedral_angle_d7.704602
X-RAY DIFFRACTIONf_chiral_restr0.06666
X-RAY DIFFRACTIONf_plane_restr0.011809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.39361230.31392789X-RAY DIFFRACTION98
1.98-2.040.33151380.26842908X-RAY DIFFRACTION100
2.04-2.110.34591050.30292769X-RAY DIFFRACTION97
2.11-2.180.27281550.25032824X-RAY DIFFRACTION100
2.18-2.270.38331670.28432744X-RAY DIFFRACTION97
2.27-2.370.2731350.23162845X-RAY DIFFRACTION99
2.37-2.50.28421660.22252761X-RAY DIFFRACTION98
2.5-2.650.28811570.21962831X-RAY DIFFRACTION100
2.65-2.860.29261400.22462865X-RAY DIFFRACTION100
2.86-3.140.24481650.21152839X-RAY DIFFRACTION99
3.15-3.60.27891030.19952899X-RAY DIFFRACTION99
3.6-4.530.19421520.16942817X-RAY DIFFRACTION99
4.54-40.010.21361760.17512890X-RAY DIFFRACTION99
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)
12.11890.38440.82281.71080.23141.9398-0.0897-0.05540.30010.0271-0.0236-0.0002-0.2524-0.03560.11840.180.0021-0.00690.19980.01580.194820.452-8.904846.5146
22.00670.51740.45011.43710.47772.53950.1608-0.1136-0.49360.1531-0.038-0.12170.42850.122-0.05520.20050.0197-0.01170.17440.01850.2646-10.4842-15.691815.4557
33.4316-0.00690.56411.19290.24381.8931-0.02490.1580.0126-0.12280.0844-0.0959-0.04640.2133-0.05460.13660.00090.02110.1601-0.01640.1695-1.8968-5.462710.8099
44.0589-1.67184.73570.7079-2.13355.1680.0173-0.4910.1986-0.06590.0034-0.08440.2039-0.3209-0.00220.2502-0.01460.06170.50370.01950.2217-5.0241-15.525343.1269
52.194-0.07560.65951.9133-0.12191.86390.0727-0.38050.22910.1745-0.0566-0.0364-0.0003-0.3393-0.02550.1638-0.05040.02030.31490.00780.172117.3197-15.370454.2247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 276 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 136 )
4X-RAY DIFFRACTION4chain 'B' and (resid 137 through 183 )
5X-RAY DIFFRACTION5chain 'B' and (resid 184 through 276 )

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