[English] 日本語
Yorodumi- PDB-6z1s: Structure of Polyphenol Oxidase (mutant G292N) from Thermothelomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z1s | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Polyphenol Oxidase (mutant G292N) from Thermothelomyces thermophila | ||||||
Components | Tyrosinase-like protein | ||||||
Keywords | OXIDOREDUCTASE / polyphenol oxidase / melanin synthesis / dicopper center / extracellular | ||||||
Function / homology | Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / oxidoreductase activity / COPPER (II) ION / GLYCINE / SERINE / Tyrosinase-like protein Function and homology information | ||||||
Biological species | Thermothelomyces thermophilus ATCC 42464 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Dimarogona, M. / Nikolaivits, E. / Valmas, A. / Topakas, E. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2021 Title: Considerations Regarding Activity Determinants of Fungal Polyphenol Oxidases Based on Mutational and Structural Studies. Authors: Nikolaivits, E. / Valmas, A. / Dedes, G. / Topakas, E. / Dimarogona, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6z1s.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z1s.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1s ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1s | HTTPS FTP |
---|
-Related structure data
Related structure data | 4j3qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46573.566 Da / Num. of mol.: 1 / Mutation: G292N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermothelomyces thermophilus ATCC 42464 (fungus) Gene: MYCTH_60685 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2QLD3 |
---|
-Sugars , 2 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar |
-Non-polymers , 5 types, 369 molecules
#4: Chemical | ChemComp-MPD / ( | ||||||
---|---|---|---|---|---|---|---|
#5: Chemical | ChemComp-GLY / #6: Chemical | ChemComp-SER / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 Details: crystallization and data collection were performed by the HTX lab at EMBL Grenoble and that the crystals were automatically harvested and cryocooled with the CrystalDirect technology |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Moprheus buffer 3, amino acids mix, MPD, PEG1000, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98012 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→43.24 Å / Num. obs: 30047 / % possible obs: 86.3 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.554→1.719 Å / Num. unique obs: 1502 / CC1/2: 0.605 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J3Q Resolution: 1.53→43.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.062 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.138 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.53→43.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|