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- PDB-8g0n: FphI, Staphylococcus aureus fluorophosphonate-binding serine hydr... -

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Basic information

Entry
Database: PDB / ID: 8g0n
TitleFphI, Staphylococcus aureus fluorophosphonate-binding serine hydrolases I, apo form
ComponentsFluorophosphonate-binding serine hydrolase I
KeywordsHYDROLASE / FphI / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase
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 USA300-0114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsFellner, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Capability Build Funding - New Zealand Synchrotron Group Ltd New Zealand
CitationJournal: Proteins / Year: 2024
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
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 hydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7704
Polymers27,6861
Non-polymers843
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.457, 60.742, 76.380
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 Fluorophosphonate-binding serine hydrolase I


Mass: 27686.197 Da / Num. of mol.: 1 / Fragment: N-terminal GPG from expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus USA300-0114 (bacteria)
Strain: USA300 / Gene: est_1 / Plasmid: F1012 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X5DUZ9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 ul 10.2 mg/ml FphI (20mM Tris pH 8.0, 150mM NaCl) were mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 200mM Magnesium chloride hexahydrate, 100mM MES pH 6.0 ...Details: 0.2 ul 10.2 mg/ml FphI (20mM Tris pH 8.0, 150mM NaCl) were mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 200mM Magnesium chloride hexahydrate, 100mM MES pH 6.0 and 20% w/v PEG 6000. Crystal appeared within a day at 16C and grew until day 2.5. Crystal was incubated for ~10s in a solution of ~25% glycerol, 75% reservoir prior to freezing.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.14→47.54 Å / Num. obs: 87208 / % possible obs: 98.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.016 / Rrim(I) all: 0.049 / Χ2: 1.02 / Net I/σ(I): 19.7 / Num. measured all: 825837
Reflection shellResolution: 1.14→1.16 Å / % possible obs: 82.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.837 / Num. measured all: 23112 / Num. unique obs: 3513 / CC1/2: 0.785 / Rpim(I) all: 0.336 / Rrim(I) all: 0.907 / Χ2: 1.05 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimless0.7.8data scaling
XDS20220220data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→47.54 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1451 4304 4.94 %
Rwork0.1318 --
obs0.1324 87099 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 3 228 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.981
X-RAY DIFFRACTIONf_dihedral_angle_d5.362309
X-RAY DIFFRACTIONf_chiral_restr0.082320
X-RAY DIFFRACTIONf_plane_restr0.008406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.36381150.34892165X-RAY DIFFRACTION79
1.15-1.170.30021340.28132477X-RAY DIFFRACTION90
1.17-1.180.26891550.22952708X-RAY DIFFRACTION99
1.18-1.190.211390.18412786X-RAY DIFFRACTION100
1.19-1.210.16611340.16522769X-RAY DIFFRACTION100
1.21-1.230.18191390.14632769X-RAY DIFFRACTION100
1.23-1.240.13281580.13692743X-RAY DIFFRACTION100
1.24-1.260.14671260.1252771X-RAY DIFFRACTION100
1.26-1.280.13091500.12022774X-RAY DIFFRACTION100
1.28-1.30.13051420.11742744X-RAY DIFFRACTION100
1.3-1.330.14041500.12412800X-RAY DIFFRACTION100
1.33-1.350.13971380.12992749X-RAY DIFFRACTION100
1.35-1.380.1541400.13472768X-RAY DIFFRACTION100
1.38-1.40.16181440.1382765X-RAY DIFFRACTION100
1.4-1.430.16051480.11772786X-RAY DIFFRACTION100
1.43-1.470.12551540.11272766X-RAY DIFFRACTION100
1.47-1.50.12851340.10652783X-RAY DIFFRACTION100
1.5-1.550.12531540.10022755X-RAY DIFFRACTION100
1.55-1.590.12131380.09822826X-RAY DIFFRACTION100
1.59-1.640.13731380.10542769X-RAY DIFFRACTION100
1.64-1.70.12851600.11072780X-RAY DIFFRACTION100
1.7-1.770.15151330.11652817X-RAY DIFFRACTION100
1.77-1.850.13191400.11612807X-RAY DIFFRACTION100
1.85-1.950.13511620.1182774X-RAY DIFFRACTION100
1.95-2.070.12641590.11782802X-RAY DIFFRACTION100
2.07-2.230.13691450.11792816X-RAY DIFFRACTION100
2.23-2.450.12761280.12382873X-RAY DIFFRACTION100
2.45-2.810.16451450.1382839X-RAY DIFFRACTION100
2.81-3.540.13881530.13662875X-RAY DIFFRACTION100
3.54-47.540.15461490.15122939X-RAY DIFFRACTION97

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