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Yorodumi- PDB-5wsy: The complex structure of SAV606 with N-carboxymethyl-3-aminobutyrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wsy | ||||||
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Title | The complex structure of SAV606 with N-carboxymethyl-3-aminobutyrate | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / thioesterase / hotdog fold | ||||||
Function / homology | Long-chain fatty acyl-CoA thioesterase FcoT-like / Long-chain fatty acyl-CoA thioesterase, Rv0098-like superfamily / FcoT-like thioesterase domain / Chem-7UC / FcoT-like thioesterase domain-containing protein Function and homology information | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an alpha , beta-unsaturated thioester. Authors: Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wsy.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wsy.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/5wsy ftp://data.pdbj.org/pub/pdb/validation_reports/ws/5wsy | HTTPS FTP |
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-Related structure data
Related structure data | 5wsxC 2pfcS 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
#1: Protein | Mass: 19606.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: SAVERM_606 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q79ZR9 #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: 3.15 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1.0 M magnesium citrate, 0.1 M imidazole, 1% glycerol, 10 mM N-carboxymethyl-3-aminobutyrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2016 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 32063 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PFC Resolution: 2→31.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.298 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.636 Å2
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Refinement step | Cycle: 1 / Resolution: 2→31.57 Å
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