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Yorodumi- PDB-4qd9: Crystal structure of Thioesterase PA1618 from Pseudomonas aerugin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qd9 | ||||||
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Title | Crystal structure of Thioesterase PA1618 from Pseudomonas aeruginosa in complex with benzoyl-dO-CoA | ||||||
Components | Thioesterase PA1618 | ||||||
Keywords | HYDROLASE / Hotdog Fold / Thioesterase / Coenzyme A / acyl carrier protein / cytosol | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.767 Å | ||||||
Authors | Ji, T. / Allen, K.N. / Dunaway-Mariano, D. | ||||||
Citation | Journal: To be Published Title: Design and Use of an Ester Analog of CoA to Trap the Michaelis Complex in a Thioesterase Authors: Latham, J.A. / Ji, T. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qd9.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qd9.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qd9_validation.pdf.gz | 957 KB | Display | wwPDB validaton report |
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Full document | 4qd9_full_validation.pdf.gz | 967.7 KB | Display | |
Data in XML | 4qd9_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 4qd9_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/4qd9 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/4qd9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16626.814 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1618 / Plasmid: pET23-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9I3A4, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 45% PEG400, 0.1M Bis Tris, 10mM beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→37.53 Å / Num. obs: 98312 / % possible obs: 97.85 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.767→37.529 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.767→37.529 Å
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Refine LS restraints |
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LS refinement shell |
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