+Open data
-Basic information
Entry | Database: PDB / ID: 5wx7 | ||||||
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Title | Alkyldiketide-CoA synthase W332G mutant from Evodia rutaecarpa | ||||||
Components | Alkyldiketide-CoA synthase | ||||||
Keywords | TRANSFERASE / polyketidesynthase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / biosynthetic process Similarity search - Function | ||||||
Biological species | Tetradium ruticarpum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.904 Å | ||||||
Authors | Matsui, T. / Kodama, T. / Tadakoshi, T. / Morita, H. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: 2-Alkylquinolone alkaloid biosynthesis in the medicinal plant Evodia rutaecarpa involves collaboration of two novel type III polyketide synthases Authors: Matsui, T. / Kodama, T. / Mori, T. / Tadakoshi, T. / Noguchi, H. / Abe, I. / Morita, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wx7.cif.gz | 314.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wx7.ent.gz | 253.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wx7 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wx7 | HTTPS FTP |
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-Related structure data
Related structure data | 5wx3SC 5wx4C 5wx5C 5wx6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44027.695 Da / Num. of mol.: 4 / Mutation: W332G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetradium ruticarpum (plant) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1X8XLG2*PLUS #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | The sequence database references for this protein does not currently exist in the UniProt database. ...The sequence database references for this protein does not currently exist in the UniProt database. This sequence has already been deposited to GenBank as LC208543. Residues from MET (-11) to SER 0 are expression tags. This structure is W332G mutant. | |
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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: 43.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1 M MES, 0.2 M lithium sulfate, 25%(w/v) PEG3350, 10 mM CoASH |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 twin | Operator: h,-k,-h-l / Fraction: 0.03 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→47.248 Å / Num. obs: 118399 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.409 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.081 / Χ2: 1.009 / Net I/σ(I): 11.81 / Num. measured all: 403637 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WX3 Resolution: 1.904→47.248 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.96 Å2 / Biso mean: 31.5046 Å2 / Biso min: 18.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.904→47.248 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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