+Open data
-Basic information
Entry | Database: PDB / ID: 8im2 | ||||||
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Title | Crystal structure of human HPPD complexed with NTBC | ||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Enzyme / Inhibitor / Complex | ||||||
Function / homology | Function and homology information Tyrosine catabolism / 4-hydroxyphenylpyruvate dioxygenase / 4-hydroxyphenylpyruvate dioxygenase activity / tyrosine catabolic process / L-phenylalanine catabolic process / Golgi membrane / endoplasmic reticulum membrane / protein homodimerization activity / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Dong, J. / Lin, H.-Y. / Yang, G.-F. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2023 Title: Structure-based discovery of pyrazole-benzothiadiazole hybrid as human HPPD inhibitors. Authors: Dong, J. / Xiao, H. / Chen, J.N. / Zheng, B.F. / Xu, Y.L. / Chen, M.X. / 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 | 8im2.cif.gz | 868.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8im2.ent.gz | 724.4 KB | Display | PDB format |
PDBx/mmJSON format | 8im2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/8im2 ftp://data.pdbj.org/pub/pdb/validation_reports/im/8im2 | HTTPS FTP |
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-Related structure data
Related structure data | 8im3C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 44996.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPD, PPD Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P32754, 4-hydroxyphenylpyruvate dioxygenase #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-NTD / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.03M CaCl2, 0.03M MgCl2, 0.05M Tris, 0.05M Bicine, pH8.5, 25% MPD, 25% PEG 1000, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 55147 / % possible obs: 96.8 % / Redundancy: 5.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.121 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2660 / CC1/2: 0.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→29.67 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.47 / 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: 2.81→29.67 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 112.651 Å / Origin y: 10.8592 Å / Origin z: 298.3061 Å
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Refinement TLS group | Selection details: all |