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Yorodumi- PDB-5ywk: Crystal structure of Arabidopsis thaliana HPPD complexed with Ben... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ywk | |||||||||
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Title | Crystal structure of Arabidopsis thaliana HPPD complexed with Benquitrione-Methyl | |||||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / 4-hydroxyphenylpyruvate dioxygenase / Herbicide / drug discovery | |||||||||
Function / homology | Function and homology information 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å | |||||||||
Authors | Yang, W.C. / Lin, H.Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: J.Agric.Food Chem. / Year: 2021 Title: Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide. Authors: Qu, R.Y. / Nan, J.X. / Yan, Y.C. / Chen, Q. / Ndikuryayo, F. / Wei, X.F. / Yang, W.C. / Lin, H.Y. / Yang, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ywk.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywk.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ywk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ywk_validation.pdf.gz | 985.3 KB | Display | wwPDB validaton report |
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Full document | 5ywk_full_validation.pdf.gz | 994.4 KB | Display | |
Data in XML | 5ywk_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 5ywk_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywk ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywk | HTTPS FTP |
-Related structure data
Related structure data | 6m6dC 1tfzS S: Starting model for refinement 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: 48873.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase #2: Chemical | #3: Chemical | #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: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 291.16 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 33% PEG 400, 0.1M sodium chloride, 0.1M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97881 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97881 Å / Relative weight: 1 |
Reflection | Resolution: 2.804→50 Å / Num. obs: 22388 / % possible obs: 97 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.89 |
Reflection shell | Resolution: 2.804→2.904 Å / Redundancy: 13 % / Rmerge(I) obs: 0.242 / Num. unique obs: 1120 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TFZ Resolution: 2.804→38.519 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.804→38.519 Å
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Refine LS restraints |
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LS refinement shell |
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