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Yorodumi- PDB-8g0n: FphI, Staphylococcus aureus fluorophosphonate-binding serine hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g0n | ||||||
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Title | FphI, Staphylococcus aureus fluorophosphonate-binding serine hydrolases I, apo form | ||||||
Components | Fluorophosphonate-binding serine hydrolase I | ||||||
Keywords | HYDROLASE / FphI / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase | ||||||
Function / homology | Esterase/lipase / carboxylesterase / Serine aminopeptidase, S33 / carboxylesterase activity / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold / Alpha/beta fold hydrolase Function and homology information | ||||||
Biological species | Staphylococcus aureus USA300-0114 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Fellner, M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: FphI, Staphylococcus aureus fluorophosphonate-binding serine hydrolases I, 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 | 8g0n.cif.gz | 171.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g0n.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 8g0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g0n ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g0n | 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: 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 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. |
-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: 0.9536 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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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: 1.14→47.54 Å
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Refine LS restraints |
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LS refinement shell |
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