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

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Basic information

Entry
Database: PDB / ID: 8sbq
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, fluorophosphonate JB101 bound
ComponentsFluorophosphonate-binding serine hydrolases E
KeywordsHYDROLASE / FphE / Staphylococcus aureus fluorophosphonate-binding serine hydrolases E / fluorophosphonate JB101 bound
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 USA100-CA-126 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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, fluorophosphonate JB101 bound
Authors: Fellner, M.
History
DepositionApr 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

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Assembly

Deposited unit
A: Fluorophosphonate-binding serine hydrolases E
B: Fluorophosphonate-binding serine hydrolases E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3507
Polymers62,5502
Non-polymers8005
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13640 Å2
ΔGint-117 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.936, 74.574, 73.862
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluorophosphonate-binding serine hydrolases E


Mass: 31275.100 Da / Num. of mol.: 2 / Fragment: N-terminal GPG from expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA100-CA-126 (bacteria)
Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-ZUV / ethyl (R)-(10-{[(but-3-yn-1-yl)carbamoyl]oxy}decyl)phosphonofluoridate


Mass: 363.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H31FNO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 534 / 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: 40.46 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20uL 25.0 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL fluorophosphonate molecule (10mM in DMSO) and incubated at 4C overnight. 0.2 ul 21.7 mg/ml FphE-fluorophosphonate ...Details: 20uL 25.0 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL fluorophosphonate molecule (10mM in DMSO) and incubated at 4C overnight. 0.2 ul 21.7 mg/ml FphE-fluorophosphonate were mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 180mM Magnesium chloride hexahydrate, 100mM Tris pH 8.0, 22.5% PEG 2000 MME. Crystal appeared within a day at 16C and grew until day 3. 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: 1.49→46.7 Å / Num. obs: 81242 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.15 / Χ2: 1.1 / Net I/σ(I): 8 / Num. measured all: 1076479
Reflection shellResolution: 1.49→1.52 Å / % possible obs: 88.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 1.19 / Num. measured all: 30839 / Num. unique obs: 3577 / CC1/2: 0.643 / Rpim(I) all: 0.406 / Rrim(I) all: 1.262 / Χ2: 1.28 / Net I/σ(I) obs: 1.2

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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: 1.5→40.09 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 4130 5.09 %
Rwork0.166 --
obs0.1672 81176 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 49 534 4969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064656
X-RAY DIFFRACTIONf_angle_d0.9146330
X-RAY DIFFRACTIONf_dihedral_angle_d10.454653
X-RAY DIFFRACTIONf_chiral_restr0.077682
X-RAY DIFFRACTIONf_plane_restr0.008840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.32941190.31092423X-RAY DIFFRACTION90
1.52-1.540.27181600.26432570X-RAY DIFFRACTION100
1.54-1.550.26121570.24692656X-RAY DIFFRACTION100
1.55-1.580.22671500.22362675X-RAY DIFFRACTION100
1.58-1.60.26231370.21092631X-RAY DIFFRACTION100
1.6-1.620.21271560.21432644X-RAY DIFFRACTION100
1.62-1.640.22251800.19562616X-RAY DIFFRACTION100
1.64-1.670.23521480.19612658X-RAY DIFFRACTION100
1.67-1.70.19381090.18862689X-RAY DIFFRACTION100
1.7-1.730.21721280.18512678X-RAY DIFFRACTION100
1.73-1.760.21581450.18232663X-RAY DIFFRACTION100
1.76-1.790.21051320.17992628X-RAY DIFFRACTION100
1.79-1.830.21251300.18362673X-RAY DIFFRACTION100
1.83-1.870.22721520.1772678X-RAY DIFFRACTION100
1.87-1.910.22991510.18072635X-RAY DIFFRACTION100
1.91-1.960.18981410.17642715X-RAY DIFFRACTION100
1.96-2.010.20751370.16922617X-RAY DIFFRACTION100
2.01-2.070.17651070.16982707X-RAY DIFFRACTION100
2.07-2.140.19791460.1662678X-RAY DIFFRACTION100
2.14-2.210.20511520.16862657X-RAY DIFFRACTION100
2.21-2.30.2051280.17382655X-RAY DIFFRACTION100
2.3-2.410.20011330.17312706X-RAY DIFFRACTION100
2.41-2.530.21351320.17912661X-RAY DIFFRACTION100
2.53-2.690.19041490.17872676X-RAY DIFFRACTION100
2.69-2.90.22341700.17562652X-RAY DIFFRACTION100
2.9-3.190.18111270.17042689X-RAY DIFFRACTION100
3.19-3.660.18051660.15082670X-RAY DIFFRACTION100
3.66-4.60.13671450.12852701X-RAY DIFFRACTION100
4.6-40.090.15941430.14762745X-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)
11.11210.21580.20620.8357-0.01021.19530.0112-0.02580.1135-0.0099-0.01070.0295-0.05950.02490.00720.11050.00630.0150.1034-0.00240.1302-3.9745-11.01487.5107
21.01720.53150.41131.4770.61652.58370.04080.0399-0.1402-0.018-0.06410.0070.20910.08260.03470.16170.02070.00660.1652-0.01880.2025-32.0751-15.1118-24.1972
31.3835-0.1065-0.2951.16220.50232.2910.00050.05420.0521-0.06060.0163-0.0903-0.0680.2111-0.01610.16950.0053-0.00810.165-0.01220.1654-24.7185-6.9105-24.6075
40.9580.2330.29871.3350.43512.58510.0186-0.18870.10010.1304-0.05230.1098-0.0456-0.22870.01640.1525-0.01110.01960.1536-0.01180.1522-9.1478-15.916416.1935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 276 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 152 )
4X-RAY DIFFRACTION4chain 'B' and (resid 153 through 276 )

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