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Open data
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Basic information
Entry | Database: PDB / ID: 7x7l | ||||||
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Title | Crystal structure of ZmHPPD-Y13161 complex | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / inhibitor / complex | ||||||
Function / homology | ![]() 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, H.-Y. / Dong, J. / 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 | ![]() | 319.8 KB | Display | ![]() |
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PDB format | ![]() | 251.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 70.6 KB | Display | |
Data in CIF | ![]() | 102 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cqrC ![]() 7cqsC ![]() 7x5rC ![]() 7x5sC ![]() 7x5uC ![]() 7x5wC ![]() 7x5xC ![]() 7x6mC ![]() 7x6nC ![]() 7x8dC ![]() 7x8eC ![]() 7xntC ![]() 1sp8S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46981.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: A0A1D6H1G0 #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-94L / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium acetate 4.6, 8% w/v PEG 4000 |
-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: Feb 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.887→50 Å / Num. obs: 109886 / % possible obs: 92.7 % / Redundancy: 1.8 % / CC1/2: 0.976 / Rmerge(I) obs: 0.105 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.887→2 Å / Rmerge(I) obs: 0.316 / Num. unique obs: 8132 / CC1/2: 0.816 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SP8 Resolution: 1.887→45.615 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 21.78 / 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: 1.887→45.615 Å
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Refine LS restraints |
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LS refinement shell |
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