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Yorodumi- PDB-8sbq: FphE, Staphylococcus aureus fluorophosphonate-binding serine hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sbq | ||||||
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Title | FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, fluorophosphonate JB101 bound | ||||||
Components | Fluorophosphonate-binding serine hydrolases E | ||||||
Keywords | HYDROLASE / FphE / Staphylococcus aureus fluorophosphonate-binding serine hydrolases E / fluorophosphonate JB101 bound | ||||||
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 USA100-CA-126 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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, fluorophosphonate JB101 bound 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 | 8sbq.cif.gz | 246.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sbq.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 8sbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbq ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbq | 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.: 2 / Fragment: N-terminal GPG from expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA100-CA-126 (bacteria) Gene: SAUSA300_2518 / Plasmid: F1010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FDS6, Hydrolases #2: Chemical | Mass: 363.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H31FNO4P / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20uL 25.0 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL fluorophosphonate molecule (10mM in DMSO) and incubated at 4C overnight. 0.2 ul 21.7 mg/ml FphE-fluorophosphonate ...Details: 20uL 25.0 mg/ml FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL fluorophosphonate molecule (10mM in DMSO) and incubated at 4C overnight. 0.2 ul 21.7 mg/ml FphE-fluorophosphonate were mixed with 0.2 ul of reservoir solution. Sitting drop reservoir contained 25 ul of 180mM Magnesium chloride hexahydrate, 100mM Tris pH 8.0, 22.5% PEG 2000 MME. Crystal appeared within a day at 16C and grew until day 3. 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: Dec 1, 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: 1.49→46.7 Å / Num. obs: 81242 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.15 / Χ2: 1.1 / Net I/σ(I): 8 / Num. measured all: 1076479 |
Reflection shell | Resolution: 1.49→1.52 Å / % possible obs: 88.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 1.19 / Num. measured all: 30839 / Num. unique obs: 3577 / CC1/2: 0.643 / Rpim(I) all: 0.406 / Rrim(I) all: 1.262 / Χ2: 1.28 / Net I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.09 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.96 / 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: 1.5→40.09 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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