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- PDB-5xgk: Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xgk | |||||||||
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Title | Crystal structure of Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase (AtHPPD) complexed with its substrate 4-hydroxyphenylpyruvate acid (HPPA) | |||||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase | |||||||||
![]() | OXIDOREDUCTASE / 4-Hydroxyphenylpyruvate Dioxygenase / catalytic mechanism / drug discovery | |||||||||
Function / homology | ![]() 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / Golgi membrane / endoplasmic reticulum membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yang, G.F. / Yang, W.C. / Lin, H.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery. Authors: Lin, H.Y. / Chen, X. / Chen, J.N. / Wang, D.W. / Wu, F.X. / Lin, S.Y. / Zhan, C.G. / Wu, J.W. / Yang, W.C. / Yang, G.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.5 KB | Display | ![]() |
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PDB format | ![]() | 231.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.2 KB | Display | ![]() |
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Full document | ![]() | 497.2 KB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 72.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yy6C ![]() 1tfzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48873.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase #2: Chemical | ChemComp-TYF / ( | #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M NaAc, 0.1M NaCl, 36% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2015 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 42651 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.117 / Net I/σ(I): 8.19 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 2170 / CC1/2: 0.828 / Rpim(I) all: 0.312 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TFZ Resolution: 2.8→44.24 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.24 Å
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Refine LS restraints |
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LS refinement shell |
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