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Yorodumi- PDB-8t87: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t87 | ||||||
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Title | FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, unbound dimer crystal form 1 | ||||||
Components | Fluorophosphonate-binding serine hydrolase E | ||||||
Keywords | HYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase | ||||||
Function / homology | Hydrolases / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Uncharacterized hydrolase SAUSA300_2518 Function and homology information | ||||||
Biological species | Staphylococcus aureus USA300-0114 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Fellner, M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections. Authors: Jo, J. / Upadhyay, T. / Woods, E.C. / Park, K.W. / Pedowitz, N.J. / Jaworek-Korjakowska, J. / Wang, S. / Valdez, T.A. / Fellner, M. / Bogyo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t87.cif.gz | 329.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t87.ent.gz | 273.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/8t87 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/8t87 | HTTPS FTP |
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-Related structure data
Related structure data | 8t88C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31275.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-0114 (bacteria) Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.83 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 ul 15.2 mg/ml FphE (9 mM HEPES pH 7.5, 87 mM NaCl, 13% DMSO) mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 0.18 M Magnesium chloride, 0.1 M Tris pH 7. ...Details: 0.2 ul 15.2 mg/ml FphE (9 mM HEPES pH 7.5, 87 mM NaCl, 13% DMSO) mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 0.18 M Magnesium chloride, 0.1 M Tris pH 7.5, 22.5 % w/v Polyethylene glycol monomethyl ether 2000. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→46.78 Å / Num. obs: 60409 / % possible obs: 98.4 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.026 / Rrim(I) all: 0.063 / Χ2: 0.99 / Net I/σ(I): 12.9 / Num. measured all: 359349 |
Reflection shell | Resolution: 1.62→1.65 Å / % possible obs: 88.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.18 / Num. measured all: 15655 / Num. unique obs: 2673 / CC1/2: 0.597 / Rpim(I) all: 0.528 / Rrim(I) all: 1.296 / Χ2: 0.92 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→38.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→38.73 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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