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- PDB-8g49: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8g49
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound
ComponentsFluorophosphonate-binding serine hydrolase E
KeywordsHYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / covalent / oxadiazolone / oxadiazole
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-CA-263 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFellner, M. / Bakker, A.T. / Martin, N.I. / Stelt, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: To be published
Title: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound
Authors: Fellner, M. / Bakker, A.T. / Martin, N.I. / Stelt, M.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6952
Polymers31,2751
Non-polymers4191
Water3,297183
1
A: Fluorophosphonate-binding serine hydrolase E
hetero molecules

A: Fluorophosphonate-binding serine hydrolase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3894
Polymers62,5502
Non-polymers8392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13080 Å2
ΔGint-97 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.434, 46.434, 218.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

21A-559-

HOH

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Components

#1: Protein Fluorophosphonate-binding serine hydrolase E


Mass: 31275.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-CA-263 (bacteria)
Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-YKF / methyl 2-formyl-2-[3-methyl-4-(3-phenoxybenzamido)phenyl]hydrazine-1-carboxylate


Mass: 419.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 65uL 16.3 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 7.5uL compound3 (10mM in DMSO) and incubated at 4C overnight. 0.15 ul FphE-compound3 solution was mixed with 0.3 ul of ...Details: 65uL 16.3 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 7.5uL compound3 (10mM in DMSO) and incubated at 4C overnight. 0.15 ul FphE-compound3 solution was mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 160mM potassium thiocyanate, 180mM Tris pH 8.5, 20% PEG 2000 MME. Crystal appeared within 2.5 days at 16C. It 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: Aug 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→43.67 Å / Num. obs: 37428 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.022 / Rrim(I) all: 0.084 / Χ2: 0.97 / Net I/σ(I): 15 / Num. measured all: 505683
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 95.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 1.281 / Num. measured all: 12794 / Num. unique obs: 1700 / CC1/2: 0.581 / Rpim(I) all: 0.485 / Rrim(I) all: 1.373 / Χ2: 0.94 / 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: 1.6→39.55 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 1875 5.02 %
Rwork0.1754 --
obs0.1766 37330 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 31 183 2403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112301
X-RAY DIFFRACTIONf_angle_d1.2283128
X-RAY DIFFRACTIONf_dihedral_angle_d16.18859
X-RAY DIFFRACTIONf_chiral_restr0.074336
X-RAY DIFFRACTIONf_plane_restr0.013414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32051390.34122551X-RAY DIFFRACTION97
1.64-1.690.30251380.26972644X-RAY DIFFRACTION99
1.69-1.740.24441630.22922683X-RAY DIFFRACTION100
1.74-1.810.24411480.20342677X-RAY DIFFRACTION100
1.81-1.880.24211250.18242710X-RAY DIFFRACTION100
1.88-1.970.23821510.18152680X-RAY DIFFRACTION100
1.97-2.070.21041450.18312713X-RAY DIFFRACTION100
2.07-2.20.21411440.18722742X-RAY DIFFRACTION100
2.2-2.370.17371490.16192713X-RAY DIFFRACTION100
2.37-2.610.20321200.17832767X-RAY DIFFRACTION100
2.61-2.980.18071420.18442778X-RAY DIFFRACTION100
2.98-3.760.20721410.172816X-RAY DIFFRACTION100
3.76-39.550.17461700.15512981X-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)
11.81760.56390.01991.804-0.2233.05930.0031-0.10970.1334-0.0483-0.0004-0.1165-0.04460.21590.00140.11960.0569-0.00290.1981-0.02240.20280.965928.0768-18.3727
23.9808-2.35683.19550.4003-1.98262.22080.1482-0.3721-0.0262-0.1110.00030.04790.2921-0.4475-0.13230.25440.0106-0.03370.39450.01980.33331.70027.89188.6555
30.9268-0.13250.33072.1517-0.16473.29840.1218-0.115-0.10850.009-0.0707-0.27240.48870.2866-0.05690.19450.0641-0.01670.22040.03460.201925.62130.354321.8183
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 276 )

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