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Open data
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Basic information
Entry | Database: PDB / ID: 7xnt | ||||||
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Title | Crystal structure of PfHPPD-Y13161 complex | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase | ||||||
![]() | OXIDOREDUCTASE / Inhibitor / Complex | ||||||
Function / homology | ![]() aromatic amino acid metabolic process / 4-hydroxyphenylpyruvate dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 276.8 KB | Display | ![]() |
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PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 75.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cqrC ![]() 7cqsC ![]() 7x5rC ![]() 7x5sC ![]() 7x5uC ![]() 7x5wC ![]() 7x5xC ![]() 7x6mC ![]() 7x6nC ![]() 7x7lC ![]() 7x8dC ![]() 7x8eSC 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
#1: Protein | Mass: 40094.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A0W0HIR1 #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-94L / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 20% w/v PEG 6000 |
-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 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 130085 / % possible obs: 97.9 % / Redundancy: 3.47 % / CC1/2: 0.9795 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.82→1.87 Å / Rmerge(I) obs: 1.356 / Num. unique obs: 9505 / CC1/2: 0.277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7X8E Resolution: 1.822→34.897 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.44 / 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: 1.822→34.897 Å
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Refine LS restraints |
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LS refinement shell |
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