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Yorodumi- PDB-6eew: Crystal structure of Catharanthus roseus tryptophan decarboxylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eew | ||||||
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Title | Crystal structure of Catharanthus roseus tryptophan decarboxylase in complex with L-tryptophan | ||||||
Components | Aromatic-L-amino-acid decarboxylase | ||||||
Keywords | LYASE / Aromatic Amino Acid Decarboxylase | ||||||
Function / homology | Function and homology information L-tryptophan decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / amino acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Catharanthus roseus (Madagascar periwinkle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05002080844 Å | ||||||
Authors | Torrens-Spence, M.P. / Chiang, Y. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. Authors: Torrens-Spence, M.P. / Chiang, Y.C. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K. #1: Journal: Biorxiv / Year: 2019 Title: Structural basis for independent origins of new catalytic machineries in plant AAAD proteins Authors: Torrens-Spence, M.P. / Chiang, Y.-C. / Smith, T. / Vicent, M.A. / 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 | 6eew.cif.gz | 851.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eew.ent.gz | 651.8 KB | Display | PDB format |
PDBx/mmJSON format | 6eew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eew_validation.pdf.gz | 488.8 KB | Display | wwPDB validaton report |
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Full document | 6eew_full_validation.pdf.gz | 525.3 KB | Display | |
Data in XML | 6eew_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 6eew_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/6eew ftp://data.pdbj.org/pub/pdb/validation_reports/ee/6eew | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56509.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Gene: TDC / Production host: Escherichia coli (E. coli) References: UniProt: P17770, aromatic-L-amino-acid decarboxylase #2: Chemical | ChemComp-TRP / #3: Chemical | ChemComp-CA / #4: 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.22M calcium chloride and 12% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→133.19 Å / Num. obs: 256582 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.3745259133 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / CC1/2: 0.855 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 2.05002080844→133.181944267 Å / SU ML: 0.404291219254 / Cross valid method: THROUGHOUT / σ(F): 1.32630353466 / Phase error: 37.340059999
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.5104999198 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05002080844→133.181944267 Å
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Refine LS restraints |
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LS refinement shell |
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