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- PDB-8g48: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8g48
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, dimeric apo form
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-CA-263 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFellner, 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, dimeric apo form
Authors: Fellner, M.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorophosphonate-binding serine hydrolase E


Theoretical massNumber of molelcules
Total (without water)31,2751
Polymers31,2751
Non-polymers00
Water2,468137
1
A: Fluorophosphonate-binding serine hydrolase E

A: Fluorophosphonate-binding serine hydrolase E


Theoretical massNumber of molelcules
Total (without water)62,5502
Polymers62,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area12140 Å2
ΔGint-76 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.941, 53.820, 121.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 ul 1.9 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 200mM Magnesium chloride hexahydrate, 100mM Tris ...Details: 0.3 ul 1.9 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 200mM Magnesium chloride hexahydrate, 100mM Tris pH 8.5, 25% PEG 2000 MME. Crystal appeared within ~30 days at 16C. 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: Jun 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→41.94 Å / Num. obs: 20746 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Χ2: 0.9 / Net I/σ(I): 9.7 / Num. measured all: 126180
Reflection shellResolution: 1.95→2 Å / % possible obs: 95.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.802 / Num. measured all: 8309 / Num. unique obs: 1384 / CC1/2: 0.717 / Rpim(I) all: 0.352 / Rrim(I) all: 0.878 / Χ2: 0.77 / Net I/σ(I) obs: 2.1

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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: 1.95→41.94 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1010 4.88 %
Rwork0.1824 --
obs0.1844 20700 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 0 137 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.947
X-RAY DIFFRACTIONf_dihedral_angle_d6.082297
X-RAY DIFFRACTIONf_chiral_restr0.056332
X-RAY DIFFRACTIONf_plane_restr0.009401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.30931510.23632678X-RAY DIFFRACTION98
2.05-2.180.28141390.21322796X-RAY DIFFRACTION100
2.18-2.350.24211360.19192795X-RAY DIFFRACTION100
2.35-2.580.25241530.19472774X-RAY DIFFRACTION100
2.58-2.960.25931550.19782804X-RAY DIFFRACTION100
2.96-3.730.22311590.17432822X-RAY DIFFRACTION100
3.73-41.940.17751170.16583021X-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)
11.52320.46760.44061.5650.29882.4025-0.05150.1113-0.0318-0.08490.00920.0964-0.0934-0.35210.04670.2140.02130.0120.297-0.01630.2667-14.6457-14.289215.439
22.98390.908-2.66260.5018-0.6892.6530.0147-0.3666-0.11520.04180.0497-0.16630.52450.8992-0.10770.41070.0237-0.03750.3963-0.00660.37113.482912.0716-7.3474
31.2016-0.0605-0.08441.7532-0.10682.6094-0.0343-0.03340.0504-0.1424-0.0312-0.0356-0.0206-0.12160.06830.17780.0093-0.0140.1813-0.01210.238-5.538916.4424-19.9811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 154 )
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 276 )

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