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Open data
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Basic information
Entry | Database: PDB / ID: 8h6a | ||||||
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Title | Crystal structure of AtHPPD complexed with YH21477 | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / Inihbitor / Complex | ||||||
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. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of AtHPPD complexed with YH20702 Authors: 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 | ![]() | 98 KB | Display | ![]() |
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PDB format | ![]() | 70.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.8 KB | Display | ![]() |
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Full document | ![]() | 796.4 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h6bC ![]() 8gwdS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45952.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-KWI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris/Bicine pH 8.5, 15% (v/v) MPD, 15% (w/v) PEG 1000, 15% (w/v) PEG 3350, 0.03M NaBr, 0.03M NaF, 0.03M NaI |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 50076 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.071 / Num. unique obs: 7754 / CC1/2: 0.802 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8GWD Resolution: 1.601→34.426 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.87 / 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: 1.601→34.426 Å
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Refine LS restraints |
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LS refinement shell |
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