+Open data
-Basic information
Entry | Database: PDB / ID: 6kho | ||||||
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Title | Crystal structure of Oryza sativa TDC with PLP | ||||||
Components | Tryptophan decarboxylase 1 | ||||||
Keywords | LYASE / amino acid decarboxylase / TRANSFERASE | ||||||
Function / homology | Function and homology information serotonin biosynthetic process from tryptophan / L-tryptophan decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / carboxy-lyase activity / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.972 Å | ||||||
Authors | Zhou, Y.Z. / Liao, L.J. / Liu, X.K. / Guo, Y. / Zhao, Y.C. / Zeng, Z.X. | ||||||
Citation | Journal: J Adv Res / Year: 2020 Title: Crystal structure ofOryza sativaTDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis. Authors: Zhou, Y. / Liao, L. / Liu, X. / Liu, B. / Chen, X. / Guo, Y. / Huang, C. / Zhao, Y. / Zeng, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kho.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kho.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kho_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6kho_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6kho_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 6kho_validation.cif.gz | 57.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/6kho ftp://data.pdbj.org/pub/pdb/validation_reports/kh/6kho | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55762.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: TDC1, Os08g0140300, LOC_Os08g04540, OJ1368_G08.14, OsJ_25993 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q6ZJK7, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 5 types, 520 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.4 Å3/Da / Density % sol: 63.85 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: PEG 1000, Imidazole/Hydrochloric acid, Calcium acetate PH range: 7.2-8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 98063 / % possible obs: 97.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.97→2.03 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.476 / Num. unique obs: 9359 / CC1/2: 0.844 / Rsym value: 0.625 / % possible all: 93.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.972→42.717 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.32 Å2 / Biso mean: 37.1049 Å2 / Biso min: 20.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.972→42.717 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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