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Yorodumi- PDB-8g49: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g49 | ||||||
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Title | FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound | ||||||
Components | Fluorophosphonate-binding serine hydrolase E | ||||||
Keywords | HYDROLASE / FphE / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase / covalent / oxadiazolone / oxadiazole | ||||||
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-CA-263 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Fellner, M. / Bakker, A.T. / Martin, N.I. / Stelt, M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To be published Title: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone compound 3 bound Authors: Fellner, M. / Bakker, A.T. / Martin, N.I. / Stelt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g49.cif.gz | 176.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g49.ent.gz | 141.7 KB | Display | PDB format |
PDBx/mmJSON format | 8g49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/8g49 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/8g49 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31275.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-CA-263 (bacteria) Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases |
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#2: Chemical | ChemComp-YKF / Mass: 419.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N3O5 / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.39 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 65uL 16.3 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 7.5uL compound3 (10mM in DMSO) and incubated at 4C overnight. 0.15 ul FphE-compound3 solution was mixed with 0.3 ul of ...Details: 65uL 16.3 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 7.5uL compound3 (10mM in DMSO) and incubated at 4C overnight. 0.15 ul FphE-compound3 solution was mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 160mM potassium thiocyanate, 180mM Tris pH 8.5, 20% PEG 2000 MME. Crystal appeared within 2.5 days at 16C. It was frozen in a solution of ~25% Ethylene glycol, 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: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.67 Å / Num. obs: 37428 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.022 / Rrim(I) all: 0.084 / Χ2: 0.97 / Net I/σ(I): 15 / Num. measured all: 505683 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 95.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 1.281 / Num. measured all: 12794 / Num. unique obs: 1700 / CC1/2: 0.581 / Rpim(I) all: 0.485 / Rrim(I) all: 1.373 / Χ2: 0.94 / Net I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.55 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15 / 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: 1.6→39.55 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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