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Yorodumi- PDB-5ywg: Crystal structure of Arabidopsis thaliana HPPD complexed with Mes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ywg | ||||||
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Title | Crystal structure of Arabidopsis thaliana HPPD complexed with Mesotrione | ||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / Mesotrione / Tyrosine metabolism | ||||||
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: 2.603 Å | ||||||
Authors | Lin, H.Y. / Yang, W.C. | ||||||
Funding support | China, 1items
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Citation | Journal: FEBS J. / Year: 2019 Title: Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations. Authors: Lin, H.Y. / Yang, J.F. / Wang, D.W. / Hao, G.F. / Dong, J.Q. / Wang, Y.X. / Yang, W.C. / Wu, J.W. / Zhan, C.G. / 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 | 5ywg.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ywg.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 5ywg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/5ywg ftp://data.pdbj.org/pub/pdb/validation_reports/yw/5ywg | HTTPS FTP |
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-Related structure data
Related structure data | 6isdC 6j63C 5xgkS C: citing same article (ref.) 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: 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 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaAc pH 4.5, 0.1M NaCl, 33% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97961 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 28278 / % possible obs: 99.38 % / Redundancy: 20 % / CC1/2: 0.99 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.057 / Net I/σ(I): 12.94 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 1.297 / Num. unique obs: 1383 / CC1/2: 0.858 / Rpim(I) all: 0.148 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XGK Resolution: 2.603→35.76 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→35.76 Å
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Refine LS restraints |
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LS refinement shell |
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