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- PDB-9dro: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9dro
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone-peptide bound
ComponentsUncharacterized hydrolase SAUSA300_2518
KeywordsHYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / Oxadiazolone
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: 1.54 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor.
Authors: Wang, S. / Woods, E.C. / Jo, J. / Zhu, J. / Hansel-Harris, A. / Holcomb, M. / Llanos, M. / Pedowitz, N.J. / Upadhyay, T. / Bennett, J. / Fellner, M. / Park, K.W. / Zhang, A. / Valdez, T.A. / ...Authors: Wang, S. / Woods, E.C. / Jo, J. / Zhu, J. / Hansel-Harris, A. / Holcomb, M. / Llanos, M. / Pedowitz, N.J. / Upadhyay, T. / Bennett, J. / Fellner, M. / Park, K.W. / Zhang, A. / Valdez, T.A. / Forli, S. / Chan, A.I. / Cunningham, C.N. / Bogyo, M.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized hydrolase SAUSA300_2518
B: Uncharacterized hydrolase SAUSA300_2518
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0368
Polymers62,5502
Non-polymers4866
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-106 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.107, 74.583, 73.555
Angle α, β, γ (deg.)90.00, 90.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized hydrolase SAUSA300_2518


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-A1BA1 / methyl 2-formyl-2-phenylhydrazine-1-carboxylate


Mass: 194.187 Da / Num. of mol.: 2
Fragment: Reacted ligand: The Oxadiazolone ring is opened and a covalent bond is formed with the active site serine (a smilar ligand has been reported in PDB entry 8T88). The actual ligand has a ...Fragment: Reacted ligand: The Oxadiazolone ring is opened and a covalent bond is formed with the active site serine (a smilar ligand has been reported in PDB entry 8T88). The actual ligand has a peptide chain attached to the benzene ring that is shown but there is no density evidence, so it wss not modelled.
Source method: obtained synthetically / Formula: C9H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 uL 15 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 4 uL Oxadiazolone-peptide-ligand (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-ligand solution was mixed ...Details: 10 uL 15 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 4 uL Oxadiazolone-peptide-ligand (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-ligand solution was mixed with 0.3 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180 mM Magnesium chloride, 100 mM MES pH 6.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% Ethylene glycol, 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: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.54→47.1 Å / Num. obs: 75123 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 1.01 / Net I/σ(I): 11.9 / Num. measured all: 513296
Reflection shellResolution: 1.54→1.57 Å / % possible obs: 94.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.237 / Num. measured all: 23000 / Num. unique obs: 3496 / CC1/2: 0.56 / Rpim(I) all: 0.514 / Rrim(I) all: 1.343 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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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: 1.54→39.82 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 3604 4.8 %
Rwork0.1555 --
obs0.1568 75083 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 32 323 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014577
X-RAY DIFFRACTIONf_angle_d1.0676222
X-RAY DIFFRACTIONf_dihedral_angle_d7.019614
X-RAY DIFFRACTIONf_chiral_restr0.062673
X-RAY DIFFRACTIONf_plane_restr0.011825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.26861090.26642529X-RAY DIFFRACTION92
1.56-1.580.24361410.22992766X-RAY DIFFRACTION100
1.58-1.60.22841430.22522731X-RAY DIFFRACTION100
1.6-1.630.24741060.20162806X-RAY DIFFRACTION100
1.63-1.650.23551300.19732720X-RAY DIFFRACTION100
1.65-1.680.22181600.19782725X-RAY DIFFRACTION100
1.68-1.710.26441430.19652726X-RAY DIFFRACTION100
1.71-1.740.21151300.19512797X-RAY DIFFRACTION100
1.74-1.770.23451350.1912740X-RAY DIFFRACTION100
1.77-1.810.22711270.19562758X-RAY DIFFRACTION100
1.81-1.850.21721270.18152754X-RAY DIFFRACTION100
1.85-1.890.21221420.15862759X-RAY DIFFRACTION100
1.89-1.940.18661540.15852756X-RAY DIFFRACTION100
1.94-1.990.18351610.14762703X-RAY DIFFRACTION100
1.99-2.050.17411480.152779X-RAY DIFFRACTION100
2.05-2.120.18281470.1482723X-RAY DIFFRACTION100
2.12-2.190.1781360.15232757X-RAY DIFFRACTION100
2.19-2.280.17681500.1472735X-RAY DIFFRACTION100
2.28-2.380.17261550.14052771X-RAY DIFFRACTION100
2.38-2.510.18921530.14942736X-RAY DIFFRACTION100
2.51-2.670.19141430.152750X-RAY DIFFRACTION100
2.67-2.870.20731220.15312780X-RAY DIFFRACTION100
2.87-3.160.16161390.15542787X-RAY DIFFRACTION100
3.16-3.620.19971200.15292799X-RAY DIFFRACTION100
3.62-4.560.1481130.12992785X-RAY DIFFRACTION99
4.56-39.820.1641700.15662807X-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)
11.25450.31610.36512.0921-0.42122.5050.01120.03480.15850.0681-0.0494-0.0262-0.251-0.030.03890.1572-0.00480.01670.13540.00340.1523-1.7269-9.679.2221
25.11060.01412.74911.6984-0.21281.74070.1156-0.0178-0.72640.4487-0.0889-0.46920.65380.1207-0.12910.61380.0946-0.06760.3390.06670.5131-28.5617-25.8112-14.0525
32.14320.29810.4731.38990.86792.7653-0.0495-0.1031-0.19950.07030.0271-0.00420.2625-0.01030.03340.16360.02620.02690.12570.0080.1827-33.7647-13.4711-24.5738
42.57560.1278-0.29761.18450.7032.3556-0.1134-0.05270.0421-0.02810.1529-0.08030.01880.2452-0.03090.14420.0228-0.00390.1332-0.01860.1589-25.5759-7.0567-24.0632
51.25330.67480.79081.760.13283.25050.0758-0.2060.14440.2528-0.0740.1992-0.0156-0.5603-0.01760.1863-0.01480.03360.2342-0.01330.1906-9.0183-15.898516.3159
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 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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