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

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Basic information

Entry
Database: PDB / ID: 9com
TitleFphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 5
ComponentsFphE
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: 2.04 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, S. aureus, fluorophosphonate-binding, serine hydrolases, lipase
Authors: Fellner, M.
History
DepositionJul 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FphE
B: FphE
C: FphE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8644
Polymers93,8253
Non-polymers391
Water3,711206
1
A: FphE
B: FphE


Theoretical massNumber of molelcules
Total (without water)62,5502
Polymers62,5502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: FphE
hetero molecules

C: FphE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6284
Polymers62,5502
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)67.399, 86.797, 137.764
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 FphE


Mass: 31275.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-terminal GPG from expression tag
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Gene: SAUSA300_2518 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3 uL 13.9 mg/mL FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.2 M Potassium thiocyanate, 0.1 M TRIS pH 8.5 ...Details: 0.3 uL 13.9 mg/mL FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.2 M Potassium thiocyanate, 0.1 M TRIS pH 8.5 and 22% 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: 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: 2.04→48.17 Å / Num. obs: 51434 / % possible obs: 99.2 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.034 / Rrim(I) all: 0.076 / Χ2: 1.01 / Net I/σ(I): 11.9 / Num. measured all: 250519
Reflection shellResolution: 2.04→2.1 Å / % possible obs: 95.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 1.436 / Num. measured all: 18545 / Num. unique obs: 3773 / CC1/2: 0.522 / Rpim(I) all: 0.697 / Rrim(I) all: 1.602 / Χ2: 1.02 / 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: 2.04→43.4 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 2429 4.73 %
Rwork0.1968 --
obs0.1991 51365 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 1 206 6800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086751
X-RAY DIFFRACTIONf_angle_d0.9129163
X-RAY DIFFRACTIONf_dihedral_angle_d6.715893
X-RAY DIFFRACTIONf_chiral_restr0.055998
X-RAY DIFFRACTIONf_plane_restr0.0081205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.31331320.33142652X-RAY DIFFRACTION93
2.09-2.130.34551590.29722837X-RAY DIFFRACTION100
2.13-2.180.31251560.28862857X-RAY DIFFRACTION100
2.18-2.240.32591460.26142855X-RAY DIFFRACTION100
2.24-2.30.27911340.25372898X-RAY DIFFRACTION100
2.3-2.360.30371370.24422834X-RAY DIFFRACTION99
2.36-2.440.30131480.2432860X-RAY DIFFRACTION100
2.44-2.530.23231300.23432866X-RAY DIFFRACTION100
2.53-2.630.26751710.23952860X-RAY DIFFRACTION99
2.63-2.750.28411310.23372890X-RAY DIFFRACTION100
2.75-2.890.2661610.22352874X-RAY DIFFRACTION99
2.89-3.070.2751290.2192890X-RAY DIFFRACTION100
3.07-3.310.26861580.21572872X-RAY DIFFRACTION99
3.31-3.640.24861380.19912920X-RAY DIFFRACTION99
3.65-4.170.24341360.17542914X-RAY DIFFRACTION99
4.17-5.250.20681200.14912974X-RAY DIFFRACTION99
5.25-43.40.19091430.1573083X-RAY DIFFRACTION98
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)
13.876-0.16160.26742.7448-0.26892.50980.0211-0.4222-0.22830.0721-0.0219-0.02340.1728-0.070.00280.26680.00440.02680.34670.0480.302718.678553.160633.5522
2-0.0064-0.4505-0.26433.9551.5290.556-0.03640.0423-0.6231-0.8401-0.13040.56080.09810.14970.13110.81760.0156-0.01480.6507-0.04790.73489.393130.182210.1029
33.8511-0.9364-0.89485.29630.92812.35910.08150.2265-0.1657-0.4912-0.1556-0.01350.0756-0.11370.060.3421-0.0204-0.02090.3183-0.01370.254518.83037.605515.2096
43.7301-0.40050.14153.09840.30372.1702-0.0207-0.27630.00320.1173-0.04540.20740.0099-0.29630.07560.26440.0026-0.00160.3401-0.00510.332614.91188.803426.8937
51.2229-2.3515-0.12676.51250.72980.02770.21290.13490.3098-1.2959-0.3503-0.7273-0.1089-0.24170.19410.65870.06150.13320.57490.00890.635524.506137.500111.3699
63.32850.90610.33935.3659-0.89472.7996-0.0084-0.01560.0167-0.45570.06730.07850.0903-0.124-0.05070.3320.0208-0.00180.32160.00890.25515.763158.049722.398
73.7719-1.1106-0.31986.14370.03883.87180.04350.12720.0533-0.3525-0.3866-0.89170.1280.35970.30790.2947-0.00070.11380.3650.10090.4656-9.361721.6672-2.8544
80.0022-0.27210.00468.75232.66711.0346-0.2561-0.13130.3311-0.398-0.28561.5065-0.2132-0.28370.43450.64890.0195-0.16190.8563-0.0970.8588-28.57747.7067-6.2625
93.60990.8236-0.10987.0246-1.52712.62040.1497-0.47430.32370.7489-0.20050.5392-0.4601-0.2850.06150.47620.0016-0.03370.4624-0.0610.3448-20.754567.22166.6697
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 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 276 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 184 )
6X-RAY DIFFRACTION6chain 'B' and (resid 185 through 276 )
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 136 )
8X-RAY DIFFRACTION8chain 'C' and (resid 137 through 183 )
9X-RAY DIFFRACTION9chain 'C' and (resid 184 through 276 )

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