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

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Basic information

Entry
Database: PDB / ID: 9edj
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 9
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: 2.6 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 9
Authors: Fellner, M.
History
DepositionNov 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized hydrolase SAUSA300_2518
B: Uncharacterized hydrolase SAUSA300_2518


Theoretical massNumber of molelcules
Total (without water)62,5502
Polymers62,5502
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-88 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.315, 98.794, 102.445
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 Uncharacterized hydrolase SAUSA300_2518


Mass: 31275.100 Da / Num. of mol.: 2
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.: 24 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.3 uL 13.9 mg/mL FphE (10 mM HEPES pH 7.6, 100 mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 200 mM Potassium Thiocyanate, 100 mM Sodium ...Details: 0.3 uL 13.9 mg/mL FphE (10 mM HEPES pH 7.6, 100 mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 200 mM Potassium Thiocyanate, 100 mM Sodium acetate pH 5.5 and 25% PEG 2000 MME. Crystal 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: Jun 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.6→46.59 Å / Num. obs: 16871 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.048 / Rrim(I) all: 0.12 / Χ2: 0.97 / Net I/σ(I): 9.8 / Num. measured all: 104515
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 97.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.817 / Num. measured all: 12542 / Num. unique obs: 1962 / CC1/2: 0.86 / Rpim(I) all: 0.345 / Rrim(I) all: 0.889 / Χ2: 1.01 / Net I/σ(I) obs: 2.4

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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: 2.6→46.59 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 831 4.94 %
Rwork0.1879 --
obs0.1919 16814 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4389 0 0 24 4413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084494
X-RAY DIFFRACTIONf_angle_d1.0026100
X-RAY DIFFRACTIONf_dihedral_angle_d6.564594
X-RAY DIFFRACTIONf_chiral_restr0.056665
X-RAY DIFFRACTIONf_plane_restr0.009802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.32121300.24822556X-RAY DIFFRACTION98
2.76-2.980.36911340.24442623X-RAY DIFFRACTION100
2.98-3.280.3121460.22582646X-RAY DIFFRACTION100
3.28-3.750.31631270.20132660X-RAY DIFFRACTION100
3.75-4.720.25171640.15872672X-RAY DIFFRACTION100
4.73-46.590.2121300.16882826X-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)
11.4294-1.0278-0.29693.17340.21744.22540.08780.09130.0983-0.3331-0.11630.1411-0.0549-0.08460.02020.30490.0293-0.0080.4020.01630.3911-4.8468-23.66151.3682
23.84290.0839-0.81315.2421-0.15591.97870.349-0.64030.3330.9727-0.6362-0.3516-0.5419-0.55570.6330.83390.0612-0.09710.8084-0.10.8312-16.4759-7.300935.959
34.6325-2.2519-1.3583.21431.8062.2853-0.1349-0.33090.34860.15570.2957-0.29280.06710.1208-0.12920.41420.0322-0.06710.40670.02290.4287-22.34825.937429.4495
43.7916-1.6499-0.4972.7890.63592.16480.03620.3773-0.0775-0.1840.0490.07080.1269-0.05-0.07440.3592-0.0087-0.040.34740.01040.3536-24.30410.627520.2638
53.9102-1.2526-0.60321.85842.34843.3016-0.30170.27250.41980.11630.9267-0.2225-1.09520.6898-0.84330.6580.05830.18440.8826-0.10341.252110.3412-16.279210.116
63.7817-2.2541-1.37973.4427-0.06814.5881-0.08490.0950.1932-0.00490.142-0.29190.54690.3776-0.06990.48820.02370.02790.4245-0.02060.32374.1312-29.19033.4345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 166 )
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 183 )
6X-RAY DIFFRACTION6chain 'B' and (resid 184 through 276 )

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