+Open data
-Basic information
Entry | Database: PDB / ID: 7x5y | ||||||
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Title | Crystal structure of AtHPPD-Y14240 complex | ||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / inhibitor / complex | ||||||
Function / homology | Function and homology information 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / iron ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å | ||||||
Authors | Lin, H.-Y. / Dong, J. / Yang, G.-F. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2023 Title: Discovery of Subnanomolar Inhibitors of 4-Hydroxyphenylpyruvate Dioxygenase via Structure-Based Rational Design. Authors: Dong, J. / Dong, J. / Yu, X.H. / Yan, Y.C. / Nan, J.X. / Ye, B.Q. / Yang, W.C. / Lin, H.Y. / Yang, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x5y.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x5y.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 7x5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/7x5y ftp://data.pdbj.org/pub/pdb/validation_reports/x5/7x5y | HTTPS FTP |
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-Related structure data
Related structure data | 7x5zC 7x62C 7x64C 7x67C 7x69C 7x8hC 7x8iC 7xvhC 8howC 7cqrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Arabidopsis thaliana (thale cress) / Gene: HPD, PDS1, At1g06570, F12K11.9 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase | ||||
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#2: Chemical | ChemComp-CO / | ||||
#3: Chemical | ChemComp-HZS / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.989 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→30 Å / Num. obs: 60815 / % possible obs: 98.2 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2973 / CC1/2: 0.873 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CQR Resolution: 1.498→28.082 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.29 / 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: 1.498→28.082 Å
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Refine LS restraints |
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LS refinement shell |
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