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Yorodumi- PDB-6dxc: Crystal structure of chalcone synthase from Selaginella moellendo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dxc | ||||||
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Title | Crystal structure of chalcone synthase from Selaginella moellendorffii - S340C mutant | ||||||
Components | Chalcone synthase | ||||||
Keywords | TRANSFERASE / Thiolase / Flavonoid / Polyketide synthase | ||||||
Function / homology | Function and homology information polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Selaginella moellendorffii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å | ||||||
Authors | Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants. Authors: Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dxc.cif.gz | 430 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dxc.ent.gz | 371.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/6dxc ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dxc | HTTPS FTP |
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-Related structure data
Related structure data | 6dx7C 6dx8C 6dx9C 6dxaC 6dxbC 6dxdC 6dxeC 6dxfC C: citing same article (ref.) |
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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: 42041.430 Da / Num. of mol.: 2 / Mutation: S340C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: SELMODRAFT_271225 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D8S128 #2: 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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.1 M MOPSO (pH 6.6), 0.3 M Mg(NO3)2, 19% (v/v) PEG 4000, and 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2011 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→31.589 Å / Num. obs: 105252 / % possible obs: 95.55 % / Redundancy: 1.8 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.04892 / Rpim(I) all: 0.04892 / Rrim(I) all: 0.06919 / Net I/σ(I): 9.66 |
Reflection shell | Resolution: 1.54→1.595 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.1642 / Mean I/σ(I) obs: 3.06 / Num. unique obs: 8805 / CC1/2: 0.891 / Rpim(I) all: 0.1642 / Rrim(I) all: 0.2322 / % possible all: 80.52 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→31.589 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.27 Å2 / Biso mean: 17.6714 Å2 / Biso min: 3.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→31.589 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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