+Open data
-Basic information
Entry | Database: PDB / ID: 7cqr | ||||||
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Title | Complex structure of HPPD with Y16550 | ||||||
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: 1.947 Å | ||||||
Authors | Lin, H.Y. / Yang, G.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Adv Agrochem / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cqr.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cqr.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 7cqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/7cqr ftp://data.pdbj.org/pub/pdb/validation_reports/cq/7cqr | HTTPS FTP |
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-Related structure data
Related structure data | 7cqsC 7x5rC 7x5sC 7x5uC 7x5wC 7x5xC 7x6mC 7x6nC 7x7lC 7x8dC 7x8eC 7xntC 6jx9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44341.832 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 (E. coli) References: UniProt: P93836, 4-hydroxyphenylpyruvate dioxygenase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-GEU / |
#4: 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: 2.05 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl pH8.5, 0.1M Bicine pH8.5, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI, 25%(w/v) MPD, 25%(w/v) PEG1000, 25%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.947→30 Å / Num. obs: 26523 / % possible obs: 92.2 % / Redundancy: 3.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.947→1.98 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 6 / Num. unique obs: 1339 / CC1/2: 0.977 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JX9 Resolution: 1.947→28.113 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.86 / 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: 1.947→28.113 Å
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Refine LS restraints |
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LS refinement shell |
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