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Open data
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Basic information
Entry | Database: PDB / ID: 7x8d | ||||||
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Title | Crystal structure of AtHPPD-phenylpyruvate complex | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, J. / Lin, H.-Y. / Yang, G.-F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / He, B. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / 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 | ![]() | 95.2 KB | Display | ![]() |
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PDB format | ![]() | 67.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cqrC ![]() 7cqsSC ![]() 7x5rC ![]() 7x5sC ![]() 7x5uC ![]() 7x5wC ![]() 7x5xC ![]() 7x6mC ![]() 7x6nC ![]() 7x7lC ![]() 7x8eC ![]() 7xntC 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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1 | ![]()
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Unit cell |
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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, ![]() |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-PPY / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 42.78 % |
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Crystal grow![]() | Temperature: 293 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: Dec 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.695→50 Å / Num. obs: 42939 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.423 / Num. unique obs: 2129 / CC1/2: 0.883 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7CQS Resolution: 1.695→44.399 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.95 / 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: 1.695→44.399 Å
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Refine LS restraints |
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LS refinement shell |
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