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Yorodumi- PDB-8ik2: RhlA exhibits dual thioesterase and acyltransferase activities du... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ik2 | ||||||
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Title | RhlA exhibits dual thioesterase and acyltransferase activities during rhamnolipid biosynthesis | ||||||
Components | 3-(3-hydroxydecanoyloxy)decanoate synthase | ||||||
Keywords | HYDROLASE / thioesterase / acyltransferase / rhamnolipid biosynthesis | ||||||
Function / homology | rhamnolipid biosynthesis / acyltransferase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Alpha/Beta hydrolase fold / (3~{S})-3-oxidanyldecanoic acid / 3-(3-hydroxydecanoyloxy)decanoate synthase Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.151 Å | ||||||
Authors | Tang, T. / Fu, L.H. / Xie, W.H. / Luo, Y.Z. / Zhang, Y.T. / Si, T. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: RhlA Exhibits Dual Thioesterase and Acyltransferase Activities during Rhamnolipid Biosynthesis Authors: Tang, T. / Fu, L. / Xie, W. / Luo, Y. / Zhang, Y. / Zhang, J. / Si, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ik2.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ik2.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ik2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ik2_validation.pdf.gz | 714.4 KB | Display | wwPDB validaton report |
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Full document | 8ik2_full_validation.pdf.gz | 716 KB | Display | |
Data in XML | 8ik2_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 8ik2_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ik2 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ik2 | HTTPS FTP |
-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: 33838.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: rhlA, PA3479 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q51559, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-5UF / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.64 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: sodium/potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→19.76 Å / Num. obs: 27004 / % possible obs: 99.43 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.099 / Num. unique obs: 27004 / % possible all: 99.43 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.151→19.757 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.52 / 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: 2.151→19.757 Å
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Refine LS restraints |
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LS refinement shell |
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