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

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Basic information

Entry
Database: PDB / ID: 8ugm
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, boronic acid-based compound Z27 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: 1.65 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 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 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)63,3829
Polymers62,5502
Non-polymers8327
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-111 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.723, 73.971, 73.183
Angle α, β, γ (deg.)90.00, 91.43, 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 / Mutation: N-terminal gpg from expression tag
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-WKK / 1-benzothiophen-3-ylboronic acid


Mass: 178.016 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7BO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
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: 1.65→46.71 Å / Num. obs: 59687 / % possible obs: 99.1 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Χ2: 0.98 / Net I/σ(I): 9.4 / Num. measured all: 350545
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 84.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.944 / Num. measured all: 11116 / Num. unique obs: 2508 / CC1/2: 0.536 / Rpim(I) all: 0.494 / Rrim(I) all: 1.072 / Χ2: 0.97 / 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: 1.65→39.82 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 3011 5.05 %
Rwork0.1496 --
obs0.1516 59652 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 49 483 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014609
X-RAY DIFFRACTIONf_angle_d1.1286271
X-RAY DIFFRACTIONf_dihedral_angle_d6.426611
X-RAY DIFFRACTIONf_chiral_restr0.059675
X-RAY DIFFRACTIONf_plane_restr0.012827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.30191160.23172170X-RAY DIFFRACTION84
1.67-1.70.24921200.20222492X-RAY DIFFRACTION96
1.7-1.730.24581220.19172634X-RAY DIFFRACTION100
1.73-1.760.20291650.17832527X-RAY DIFFRACTION100
1.76-1.80.23331410.182628X-RAY DIFFRACTION100
1.8-1.830.2351420.182549X-RAY DIFFRACTION100
1.83-1.870.21781070.16322632X-RAY DIFFRACTION100
1.87-1.910.20661490.16132557X-RAY DIFFRACTION100
1.92-1.960.20681490.15522595X-RAY DIFFRACTION100
1.96-2.020.19971570.15572563X-RAY DIFFRACTION100
2.02-2.080.21231200.15692598X-RAY DIFFRACTION100
2.08-2.140.20011320.15172624X-RAY DIFFRACTION100
2.14-2.220.19751490.14792577X-RAY DIFFRACTION100
2.22-2.310.18491480.14372579X-RAY DIFFRACTION100
2.31-2.410.18051320.13592585X-RAY DIFFRACTION100
2.41-2.540.16681360.14232609X-RAY DIFFRACTION100
2.54-2.70.19891310.14922599X-RAY DIFFRACTION100
2.7-2.910.20871480.15382617X-RAY DIFFRACTION100
2.91-3.20.17161400.15532578X-RAY DIFFRACTION100
3.2-3.660.202990.13992676X-RAY DIFFRACTION100
3.66-4.610.15251420.11712618X-RAY DIFFRACTION100
4.61-39.820.17611660.15512634X-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)
10.91130.1264-0.09631.0519-0.11661.41420.06620.02640.0997-0.0226-0.0169-0.0214-0.2083-0.0024-0.04810.13750.00940.01690.09920.00870.1327-0.3377-6.71239.666
23.3941-0.81843.42850.1726-0.82323.36860.16190.13440.0435-0.0365-0.1009-0.02490.14650.1254-0.11360.2578-0.0033-0.0130.1730.02570.2341-22.5992-26.7166-6.3223
31.13120.17960.16571.36090.69432.3295-0.00480.0154-0.0168-0.0230.0325-0.040.07470.09280.00780.08910.00260.01150.09860.00450.1308-33.5633-13.3852-24.3035
41.63870.0698-0.0731.05640.26541.7829-0.04970.01870.0802-0.01280.0865-0.1169-0.08650.3426-0.02520.092-0.0196-0.00410.15120.00110.1383-25.1245-7.0405-23.8243
50.93740.08360.3561.3764-0.00962.16670.0958-0.08470.02090.0675-0.030.0950.0268-0.2611-0.06820.1138-0.0080.0090.12160.0090.1327-9.2407-16.059116.2666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 152 )
5X-RAY DIFFRACTION5chain 'B' and (resid 153 through 276 )

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