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Yorodumi- PDB-6ebn: Crystal structure of Psilocybe cubensis noncanonical aromatic ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ebn | ||||||
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Title | Crystal structure of Psilocybe cubensis noncanonical aromatic amino acid decarboxylase | ||||||
Components | non canonical aromatic amino acid decarboxylase | ||||||
Keywords | METAL BINDING PROTEIN / Aromatic Amino Acid Decarboxylase | ||||||
Function / homology | Function and homology information carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Psilocybe cubensis (magic mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96631108321 Å | ||||||
Authors | Torrens-Spence, M.P. / Chun-Ting, L. / Pluskal, T. / Chung, Y.K. / Weng, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Monoamine Biosynthesis via a Noncanonical Calcium-Activatable Aromatic Amino Acid Decarboxylase in Psilocybin Mushroom. Authors: Torrens-Spence, M.P. / Liu, C.T. / Pluskal, T. / Chung, Y.K. / 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 | 6ebn.cif.gz | 876.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ebn.ent.gz | 650.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ebn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/6ebn ftp://data.pdbj.org/pub/pdb/validation_reports/eb/6ebn | HTTPS FTP |
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-Related structure data
Related structure data | 5hsjS 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: 113510.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYB6*PLUS #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NA / #5: 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: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→123 Å / Num. obs: 169024 / % possible obs: 99.06 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.0859041966 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.58 |
Reflection shell | Resolution: 1.96→2 Å / Redundancy: 6.4 % / Num. unique obs: 7168 / CC1/2: 0.469 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HSJ Resolution: 1.96631108321→71.785 Å / SU ML: 0.21615955403 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.8935550497
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.1104722326 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96631108321→71.785 Å
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Refine LS restraints |
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LS refinement shell |
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