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Yorodumi- PDB-8g48: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g48 | ||||||
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Title | FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, dimeric apo form | ||||||
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-CA-263 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Fellner, M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, dimeric apo form Authors: Fellner, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g48.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g48.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 8g48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/8g48 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/8g48 | 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
#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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3 ul 1.9 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 200mM Magnesium chloride hexahydrate, 100mM Tris ...Details: 0.3 ul 1.9 mg/ml FphE (10mM HEPES pH 7.6, 100mM NaCl) were mixed with 0.3 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 200mM Magnesium chloride hexahydrate, 100mM Tris pH 8.5, 25% PEG 2000 MME. Crystal appeared within ~30 days at 16C. It 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: Jun 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→41.94 Å / Num. obs: 20746 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.107 / Χ2: 0.9 / Net I/σ(I): 9.7 / Num. measured all: 126180 |
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 95.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.802 / Num. measured all: 8309 / Num. unique obs: 1384 / CC1/2: 0.717 / Rpim(I) all: 0.352 / Rrim(I) all: 0.878 / Χ2: 0.77 / Net I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.94 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / 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: 1.95→41.94 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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