+Open data
-Basic information
Entry | Database: PDB / ID: 6lgt | ||||||
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Title | Complex structure of HPPD with an inhibitor Y16542 | ||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / 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: 1.794 Å | ||||||
Authors | Lin, H.Y. / Yang, W.C. / Yang, G.F. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2020 Title: Discovery of Novel Pyrazole-Quinazoline-2,4-dione Hybrids as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors. Authors: He, B. / Wu, F.X. / Yu, L.K. / Wu, L. / Chen, Q. / Hao, G.F. / 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 | 6lgt.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lgt.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lgt_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6lgt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6lgt_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6lgt_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lgt ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lgt | HTTPS FTP |
-Related structure data
Related structure data | 5ywhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48873.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD / Production host: Escherichia coli (E. coli) References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-ED3 / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaAc pH4.5, 33% PEG 400, 0.1M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.794→30 Å / Num. obs: 35392 / % possible obs: 97.3 % / Redundancy: 4 % / CC1/2: 0.985 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 1765 / CC1/2: 0.811 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YWH Resolution: 1.794→28.12 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.88 Å2 / Biso mean: 29.201 Å2 / Biso min: 10.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.794→28.12 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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