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- PDB-8t87: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8t87
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 1
ComponentsFluorophosphonate-binding serine hydrolase E
KeywordsHYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase
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 USA300-0114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections.
Authors: Jo, J. / Upadhyay, T. / Woods, E.C. / Park, K.W. / Pedowitz, N.J. / Jaworek-Korjakowska, J. / Wang, S. / Valdez, T.A. / Fellner, M. / Bogyo, M.
History
DepositionJun 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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: Fluorophosphonate-binding serine hydrolase E
B: Fluorophosphonate-binding serine hydrolase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6968
Polymers62,5502
Non-polymers1466
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.787, 74.082, 71.424
Angle α, β, γ (deg.)90.00, 91.28, 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 USA300-0114 (bacteria)
Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul 15.2 mg/ml FphE (9 mM HEPES pH 7.5, 87 mM NaCl, 13% DMSO) mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 0.18 M Magnesium chloride, 0.1 M Tris pH 7. ...Details: 0.2 ul 15.2 mg/ml FphE (9 mM HEPES pH 7.5, 87 mM NaCl, 13% DMSO) mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 0.18 M Magnesium chloride, 0.1 M Tris pH 7.5, 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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.62→46.78 Å / Num. obs: 60409 / % possible obs: 98.4 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.026 / Rrim(I) all: 0.063 / Χ2: 0.99 / Net I/σ(I): 12.9 / Num. measured all: 359349
Reflection shellResolution: 1.62→1.65 Å / % possible obs: 88.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.18 / Num. measured all: 15655 / Num. unique obs: 2673 / CC1/2: 0.597 / Rpim(I) all: 0.528 / Rrim(I) all: 1.296 / Χ2: 0.92 / Net I/σ(I) obs: 1.4

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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: 1.62→38.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 2954 4.89 %
Rwork0.1873 --
obs0.1889 60354 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 6 219 4611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114525
X-RAY DIFFRACTIONf_angle_d1.1356148
X-RAY DIFFRACTIONf_dihedral_angle_d6.424602
X-RAY DIFFRACTIONf_chiral_restr0.065669
X-RAY DIFFRACTIONf_plane_restr0.011811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.43171120.39022462X-RAY DIFFRACTION89
1.65-1.680.37291510.36952671X-RAY DIFFRACTION97
1.68-1.710.39841490.34362729X-RAY DIFFRACTION99
1.71-1.740.37211200.34182711X-RAY DIFFRACTION97
1.74-1.780.33831360.31442747X-RAY DIFFRACTION99
1.78-1.820.34511760.28632655X-RAY DIFFRACTION98
1.82-1.860.30681100.25522788X-RAY DIFFRACTION99
1.86-1.910.25711220.22452749X-RAY DIFFRACTION98
1.91-1.960.26411180.21082762X-RAY DIFFRACTION98
1.96-2.010.23541710.20382713X-RAY DIFFRACTION99
2.01-2.080.25211310.20562739X-RAY DIFFRACTION99
2.08-2.150.24431530.20212745X-RAY DIFFRACTION99
2.15-2.240.21961510.19182749X-RAY DIFFRACTION99
2.24-2.340.2241720.18172732X-RAY DIFFRACTION99
2.34-2.470.21211130.1862787X-RAY DIFFRACTION99
2.47-2.620.22271350.18472753X-RAY DIFFRACTION99
2.62-2.820.22751380.19072776X-RAY DIFFRACTION99
2.82-3.110.21540.18312784X-RAY DIFFRACTION99
3.11-3.560.22561670.17042738X-RAY DIFFRACTION99
3.56-4.480.16481220.14152811X-RAY DIFFRACTION99
4.48-38.730.17791530.16412799X-RAY DIFFRACTION98
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)
10.88370.02090.40122.0225-0.35452.109-0.06390.05660.16860.0874-0.0198-0.0788-0.35410.0090.08310.2619-0.0073-0.00480.22130.03530.2716-2.0494-9.50369.0098
22.23290.37982.45111.30390.25052.57890.21790.1179-0.6123-0.3231-0.33410.06720.83390.34060.03180.65110.1436-0.06880.47020.02660.749-28.1976-25.3263-13.9386
32.6782-0.03870.03781.52040.52873.13240.02160.0785-0.39590.05710.1565-0.33690.36340.2041-0.08130.21580.03430.00020.2006-0.07810.3233-33.3415-13.3817-24.357
42.1620.0553-0.2791.7210.7792.0320.04670.0971-0.0718-0.08630.3255-0.5350.03560.6081-0.270.19450.02540.01840.3617-0.16840.4276-23.7017-5.9289-26.0543
54.1625-2.26084.89491.0378-2.54374.35130.2627-0.2711-0.0749-0.233-0.0078-0.00970.4539-0.0969-0.19960.32120.05030.02990.472-0.00250.3949-27.3831-15.86395.9478
61.37110.27331.12462.4082-0.25972.848-0.039-0.17030.00880.33290.0322-0.0405-0.1332-0.2332-0.00650.2340.00990.01850.22150.01420.229-5.5551-15.717516.9836
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 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 183 )
6X-RAY DIFFRACTION6chain 'B' and (resid 184 through 276 )

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