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Yorodumi- PDB-6isd: Crystal structure of Arabidopsis thaliana HPPD complexed with sul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6isd | |||||||||
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Title | Crystal structure of Arabidopsis thaliana HPPD complexed with sulcotrione | |||||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 4-Hydroxyphenylpyruvate dioxygenase / Slow binding inhibitors / drug design / OXIDOREDUCTASE / OXIDOREDUCTASE-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: 2.4 Å | |||||||||
Authors | Yang, W.C. / Yang, G.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: FEBS J. / Year: 2019 Title: Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations. Authors: Lin, H.Y. / Yang, J.F. / Wang, D.W. / Hao, G.F. / Dong, J.Q. / Wang, Y.X. / Yang, W.C. / Wu, J.W. / Zhan, C.G. / 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 | 6isd.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isd.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 6isd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isd ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isd | HTTPS FTP |
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-Related structure data
Related structure data | 5ywgC 6j63C 1sp9S S: Starting model for refinement C: citing same article (ref.) |
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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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1M NaAc pH 5.0, 0.1M NaCl, 35% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 37032 / % possible obs: 99.8 % / Redundancy: 11.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.213 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.18 / Num. unique obs: 1790 / CC1/2: 0.695 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SP9 Resolution: 2.4→29.752 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.752 Å
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Refine LS restraints |
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LS refinement shell |
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