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- PDB-9c0n: FphI, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 9c0n
TitleFphI, Staphylococcus aureus fluorophosphonate-binding serine hydrolases I, apo form at room temperature
ComponentsAlpha/beta fold hydrolase
KeywordsHYDROLASE / FphI / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / room temperature / humidity / humidifier
Function / homologyEsterase/lipase / : / Serine aminopeptidase, S33 / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Alpha/Beta hydrolase fold / Alpha/beta fold hydrolase
Function and homology information
Biological speciesStaphylococcus aureus USA300-CA-263 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFellner, M. / Randall, G.T.
Funding support1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd
CitationJournal: Proteins / Year: 2025
Title: Similar but Distinct-Biochemical Characterization of the Staphylococcus aureus Serine Hydrolases FphH and FphI.
Authors: Fellner, M. / Randall, G. / Bitac, I.R.C.G. / Warrender, A.K. / Sethi, A. / Jelinek, R. / Kass, I.
History
DepositionMay 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta fold hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8475
Polymers27,6861
Non-polymers1604
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.656, 61.736, 77.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta fold hydrolase / Carboxylesterase / Esterase/lipase family protein


Mass: 27686.197 Da / Num. of mol.: 1 / Mutation: N-terminal GPG from expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-CA-263 (bacteria)
Gene: est_2, est_1, BN1321_100022, C7M54_03125, DD547_00417, EP54_01625, EQ90_13375, FAF17_11905, GO814_02325, GO941_12735, GO942_04080, GQX37_00145, HMPREF3211_01442, NCTC10702_00834, NCTC13131_ ...Gene: est_2, est_1, BN1321_100022, C7M54_03125, DD547_00417, EP54_01625, EQ90_13375, FAF17_11905, GO814_02325, GO941_12735, GO942_04080, GQX37_00145, HMPREF3211_01442, NCTC10702_00834, NCTC13131_05910, SAMEA2078260_02464, SAMEA2078588_01365, SAMEA2080344_01425, SAMEA2081063_02567, SAMEA4008575_01596, SAMEA70146418_02725
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5DUZ9, carboxylesterase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL 10 mg/mL FphI (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 200mM Calcium chloride hexahydrate, 100mM HEPES pH 7.0, 20 % w/v PEG 6000.

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: Room temperature data collection / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→48.21 Å / Num. obs: 28252 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Χ2: 1.01 / Net I/σ(I): 15.8 / Num. measured all: 146228
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.127 / Num. measured all: 6850 / Num. unique obs: 1435 / CC1/2: 0.66 / Rpim(I) all: 0.559 / Rrim(I) all: 1.263 / Χ2: 0.94 / Net I/σ(I) obs: 1.3

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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: 1.7→40.06 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.17 1395 4.95 %
Rwork0.1493 --
obs0.1504 28197 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 4 119 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012092
X-RAY DIFFRACTIONf_angle_d1.0442852
X-RAY DIFFRACTIONf_dihedral_angle_d5.306288
X-RAY DIFFRACTIONf_chiral_restr0.061306
X-RAY DIFFRACTIONf_plane_restr0.009380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.31091260.26072643X-RAY DIFFRACTION99
1.76-1.830.29161330.2342614X-RAY DIFFRACTION100
1.83-1.910.20881400.22282637X-RAY DIFFRACTION100
1.91-2.020.17911540.16552640X-RAY DIFFRACTION100
2.02-2.140.18031370.15232677X-RAY DIFFRACTION99
2.14-2.310.17071550.15542647X-RAY DIFFRACTION100
2.31-2.540.17981240.14462700X-RAY DIFFRACTION100
2.54-2.910.17721480.14982697X-RAY DIFFRACTION100
2.91-3.660.17791260.13962714X-RAY DIFFRACTION99
3.66-40.060.13851520.13172833X-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)
13.6286-1.481-0.01042.5597-0.06522.2126-0.0645-0.16720.32020.12010.0051-0.0468-0.23010.01560.04820.2225-0.0130.0070.1839-0.01120.23750.955811.105721.1209
21.2333-0.16940.66661.61620.34422.3992-0.0288-0.0255-0.14610.17310.02020.08030.08560.1031-0.0030.2252-0.01940.02480.19970.01650.22974.94910.617421.9708
35.39660.08030.67142.80951.56575.3617-0.0720.05510.8532-0.5167-0.042-0.174-0.82731.2090.09810.4902-0.23130.02860.93890.00880.510923.941512.122622.1709
43.03721.88170.61534.57950.73033.25550.0179-0.226-0.0940.54320.1014-0.60440.06921.0777-0.14460.2720.0188-0.05330.5464-0.0520.356320.9638-2.2422.0545
52.8181-0.2871-0.7963.53880.08322.76880.16550.14530.2049-0.4065-0.1079-0.2219-0.35530.2988-0.05080.3141-0.00910.03020.28480.0150.20557.68562.23664.471
63.7253.6932-0.65493.8234-0.28646.62520.0330.31770.6118-0.66410.07520.6886-0.6401-0.3677-0.06060.34330.0415-0.02190.26390.01030.3418-3.52669.85066.9641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 144 )
4X-RAY DIFFRACTION4chain 'A' and (resid 145 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 244 )

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