+Open data
-Basic information
Entry | Database: PDB / ID: 6hqi | ||||||
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Title | holo-form of polyphenol oxidase from Solanum lycopersicum | ||||||
Components | Polyphenol oxidase A, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / polyphenol oxidase / tyrosinase | ||||||
Function / homology | Function and homology information catechol oxidase / catechol oxidase activity / pigment biosynthetic process / chloroplast thylakoid lumen / metal ion binding Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Kampatsikas, I. / Bijelic, A. / Rompel, A. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Biochemical and structural characterization of tomato polyphenol oxidases provide novel insights into their substrate specificity. Authors: Kampatsikas, I. / Bijelic, A. / Rompel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hqi.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hqi.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/6hqi ftp://data.pdbj.org/pub/pdb/validation_reports/hq/6hqi | HTTPS FTP |
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-Related structure data
Related structure data | 6hqjC 5ce9S 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: 57218.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08303*PLUS, catechol oxidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-O / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM sodium citrate pH 6.6, 13% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.231 Å / Num. obs: 37575 / % possible obs: 99.95 % / Redundancy: 6.7 % / Net I/σ(I): 6.81 |
Reflection shell | Resolution: 1.85→1.92 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CE9 Resolution: 1.85→42.231 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→42.231 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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