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Yorodumi- PDB-6sla: Crystal structure of isomerase PaaG mutant - D136N with Oxepin-CoA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sla | ||||||
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Title | Crystal structure of isomerase PaaG mutant - D136N with Oxepin-CoA | ||||||
Components | Enoyl-CoA hydratase/carnithine racemase | ||||||
Keywords | ISOMERASE / phenylacetic acid catabolism / tropodithietic acid / crotonase | ||||||
Function / homology | Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Chem-LHQ / Enoyl-CoA hydratase/carnithine racemase Function and homology information | ||||||
Biological species | Thermus thermophilus JL-18 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Saleem-Batcha, R. / Spieker, M. / Teufel, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. Authors: Spieker, M. / Saleem-Batcha, R. / Teufel, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sla.cif.gz | 298.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sla.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6sla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6sla ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6sla | HTTPS FTP |
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-Related structure data
Related structure data | 6sl9C 6slbC 3hrxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 27575.875 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_0099 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H9ZNW0 #2: Chemical | ChemComp-LHQ / ~{ #3: 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: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 50 mM KH2PO4, pH 4.5, 20-22% PEG 3350, 3% (w/v) NDSB-201 and 20% glycerol (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→48.645 Å / Num. obs: 45527 / % possible obs: 96.84 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 9.82 |
Reflection shell | Resolution: 2.55→2.641 Å / Num. unique obs: 3708 / Rpim(I) all: 0.2727 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HRX Resolution: 2.55→48.645 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.696 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.132 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→48.645 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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