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Yorodumi- PDB-6slb: Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6slb | ||||||
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Title | Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-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-T3D / Enoyl-CoA hydratase/carnithine racemase Function and homology information | ||||||
Biological species | Thermus thermophilus JL-18 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 | 6slb.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6slb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6slb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6slb_validation.pdf.gz | 680.4 KB | Display | wwPDB validaton report |
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Full document | 6slb_full_validation.pdf.gz | 684.2 KB | Display | |
Data in XML | 6slb_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6slb_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/6slb ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slb | HTTPS FTP |
-Related structure data
Related structure data | 6sl9C 6slaC 3hrxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27861.174 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-T3D / (~{ |
#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: 2.04 Å3/Da / Density % sol: 39.7 % |
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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: Jun 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→44.01 Å / Num. obs: 18671 / % possible obs: 99.41 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 22.48 |
Reflection shell | Resolution: 1.88→1.947 Å / Rmerge(I) obs: 0.2998 / Num. unique obs: 1747 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HRX Resolution: 1.88→44.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.185 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145 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: 35.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→44.01 Å
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Refine LS restraints |
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LS refinement shell |
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