+Open data
-Basic information
Entry | Database: PDB / ID: 5wx4 | ||||||
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Title | Alkylquinolone synthase from Evodia rutaecarpa | ||||||
Components | alkylquinolone synthase | ||||||
Keywords | TRANSFERASE / polyketidesynthase | ||||||
Function / homology | Function and homology information biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Tetradium ruticarpum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 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 | 5wx4.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wx4.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wx4_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 5wx4_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 5wx4_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 5wx4_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/5wx4 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/5wx4 | HTTPS FTP |
-Related structure data
Related structure data | 5wx3C 5wx5C 5wx6C 5wx7C 3wd8S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 45520.020 Da / Num. of mol.: 3 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: A0A1W7GKH4*PLUS #2: 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 LC208544. Residues from MET (-11) to SER 0 are expression tags. | |
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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: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, 0.2 M Magnesium chloride, 10%(w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 69341 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5 |
-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: 3WD8 Resolution: 2.203→38.738 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.07 Å2 / Biso mean: 33.888 Å2 / Biso min: 19.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.203→38.738 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25
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