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- PDB-9d87: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9d87
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 8
ComponentsUncharacterized hydrolase SAUSA300_2518
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 subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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, unbound dimer crystal form 8
Authors: Fellner, M.
History
DepositionAug 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized hydrolase SAUSA300_2518


Theoretical massNumber of molelcules
Total (without water)31,2751
Polymers31,2751
Non-polymers00
Water21612
1
A: Uncharacterized hydrolase SAUSA300_2518

A: Uncharacterized hydrolase SAUSA300_2518


Theoretical massNumber of molelcules
Total (without water)62,5502
Polymers62,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area12310 Å2
ΔGint-87 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.698, 105.698, 105.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Uncharacterized hydrolase SAUSA300_2518


Mass: 31275.100 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 uL ~11 mg/mL FphE (10 mM HEPES pH 7.5 , 100 mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.18 M Potassium thiocyanate, 0.1 M TRIS pH ...Details: 0.3 uL ~11 mg/mL FphE (10 mM HEPES pH 7.5 , 100 mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.18 M Potassium thiocyanate, 0.1 M TRIS pH 8.5 and 22.5% w/v Polyethylene glycol monomethyl ether 2,000. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir after ~10s soaking in that solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→47.27 Å / Num. obs: 17790 / % possible obs: 99.8 % / Redundancy: 30.3 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.015 / Rrim(I) all: 0.081 / Χ2: 1.01 / Net I/σ(I): 32.8 / Num. measured all: 539288
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 98.4 % / Redundancy: 30.1 % / Rmerge(I) obs: 2.75 / Num. measured all: 50595 / Num. unique obs: 1680 / CC1/2: 0.654 / Rpim(I) all: 0.502 / Rrim(I) all: 2.796 / Χ2: 0.94 / 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: 2.3→37.37 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 864 4.87 %
Rwork0.2181 --
obs0.219 17757 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 0 12 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082245
X-RAY DIFFRACTIONf_angle_d0.9993047
X-RAY DIFFRACTIONf_dihedral_angle_d6.388297
X-RAY DIFFRACTIONf_chiral_restr0.057332
X-RAY DIFFRACTIONf_plane_restr0.009401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.35691330.33082745X-RAY DIFFRACTION98
2.44-2.630.35721350.29382778X-RAY DIFFRACTION100
2.63-2.90.3421470.32642790X-RAY DIFFRACTION100
2.9-3.310.29681770.29522794X-RAY DIFFRACTION100
3.32-4.170.24691060.22492870X-RAY DIFFRACTION100
4.18-37.370.18381660.15922916X-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)
11.55760.01130.28272.13820.66041.6991-0.0487-0.5630.06580.3040.0564-0.02370.21620.298-0.03050.53570.1319-0.03880.8287-0.1760.4732-23.4388-27.240649.4093
22.72950.74891.23960.11330.31850.4834-0.3751-0.492-0.2322-0.0415-0.3541-0.14110.0960.05190.64990.6054-0.0411-0.03951.020.16040.77963.7238-8.104246.032
30.5833-0.56890.09782.78640.482.0033-0.03410.47220.2985-0.2661-0.0104-0.0745-0.2562-0.34960.04090.5006-0.0884-0.06090.880.31310.606924.723-14.979757.6851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 276 )

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