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Yorodumi- PDB-7e0x: Crystal structure of Arabidopsis thaliana HPPD complexed with 4-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e0x | ||||||
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Title | Crystal structure of Arabidopsis thaliana HPPD complexed with 4-hydroxyphenylacetic acid | ||||||
Components | 4-hydroxyphenylpyruvate dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Enzyme / Complex / Intermediate product | ||||||
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: 1.887 Å | ||||||
Authors | Lin, H.Y. / Yang, G.F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study. Authors: Lin, H.Y. / Chen, X. / Dong, J. / Yang, J.F. / Xiao, H. / Ye, Y. / Li, L.H. / Zhan, C.G. / Yang, W.C. / 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 | 7e0x.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e0x.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 7e0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/7e0x ftp://data.pdbj.org/pub/pdb/validation_reports/e0/7e0x | HTTPS FTP |
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-Related structure data
Related structure data | 5yy6S 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: 44784.332 Da / Num. of mol.: 1 / Mutation: S267W 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-4HP / |
#4: 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: 2.38 Å3/Da / Density % sol: 43.27 % |
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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: BL17U / Wavelength: 0.9775 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 1.887→30 Å / Num. obs: 30147 / % possible obs: 96.6 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.447 / Num. unique obs: 1498 / CC1/2: 0.869 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YY6 Resolution: 1.887→28.683 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.62 / 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: 1.887→28.683 Å
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Refine LS restraints |
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LS refinement shell |
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