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Yorodumi- PDB-5eo2: Structural and biochemical characterization of the hypothetical p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eo2 | ||||||
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Title | Structural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus in complex with CoA. | ||||||
Components | thioesterase | ||||||
Keywords | HYDROLASE / Thioesterases / hypothetical protein SAV2348 / staphylococcus aureus / coenzyme A | ||||||
Function / homology | Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / COENZYME A / Uncharacterized protein / Thioesterase Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Khandokar, Y.B. / Srivastava, P. / Forwood, J.K. | ||||||
Citation | Journal: To Be Published Title: Structural and biochemical characterization of the hypothetical protein SAV2348 from Staphylococcus aureus in complex with CoA Authors: Khandokar, Y.B. / Srivastava, P. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eo2.cif.gz | 198.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eo2.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 5eo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eo2_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5eo2_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5eo2_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 5eo2_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eo2 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eo2 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19118.453 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria) Strain: Mu50 / ATCC 700699 / Gene: SAV2348 / Plasmid: pMCSG21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: A0A0H3JRH2, UniProt: A0A0H3JSY9*PLUS #2: Chemical | ChemComp-COA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M sodium acetate pH4.6, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→97.48 Å / Num. obs: 37843 / % possible obs: 99.55 % / Redundancy: 2 % / Net I/σ(I): 8.73 |
-Processing
Software |
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Refinement | Resolution: 2.5→97.48 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.895 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 40.809 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→97.48 Å
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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