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- PDB-2ycp: F448H mutant of tyrosine phenol-lyase from Citrobacter freundii i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ycp | ||||||
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Title | F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine | ||||||
![]() | TYROSINE PHENOL-LYASE | ||||||
![]() | LYASE / PYRIDOXAL 5'-PHOSPHATE DEPENDENT ENZYME / BETA-ELIMINATION | ||||||
Function / homology | ![]() tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Milic, D. / Demidkina, T.V. / Faleev, N.G. / Phillips, R.S. / Matkovic-Calogovic, D. / Antson, A.A. | ||||||
![]() | ![]() Title: Crystallographic Snapshots of Tyrosine Phenol-Lyase Show that Substrate Strain Plays a Role in C-C Bond Cleavage Authors: Milic, D. / Demidkina, T.V. / Faleev, N.G. / Phillips, R.S. / Matkovic-Calogovic, D. / Antson, A.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 750.1 KB | Display | ![]() |
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PDB format | ![]() | 622.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 86.7 KB | Display | |
Data in CIF | ![]() | 130.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ycnC ![]() 2yctC ![]() 2ez2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 51557.758 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 1893 molecules ![](data/chem/img/P61.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/P33.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/P33.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-P61 / ( #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-PG4 / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-EDO / | #7: Chemical | ChemComp-1PE / | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 448 TO HIS ENGINEERED RESIDUE IN CHAIN B, PHE 448 TO HIS ...ENGINEERED |
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Nonpolymer details | RESIDUE P61 - (2E)-3-(3-FLUORO-4-HYDROXYPHENYL)-2-{[(Z)-{3- HYDROXY- 2-METHYL-5-[(PHOSPHONOOXY) ...RESIDUE P61 - (2E)-3-(3-FLUORO-4-HYDROXYPHE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.5 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALS OF THE C. FREUNDII F448H TPL WERE GROWN AT 277 AND 293 K USING THE HANGING DROP VAPOR DIFFUSION METHOD. THE BEST CRYSTALS WERE OBTAINED BY MIXING 2 UL OF THE PROTEIN SOLUTION (18-20 ...Details: CRYSTALS OF THE C. FREUNDII F448H TPL WERE GROWN AT 277 AND 293 K USING THE HANGING DROP VAPOR DIFFUSION METHOD. THE BEST CRYSTALS WERE OBTAINED BY MIXING 2 UL OF THE PROTEIN SOLUTION (18-20 MG/ML) CONTAINING 50 MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1 MM DDT WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.5 MM PLP, 2 MM DDT, 0.4 M KCL, AND 35-38% (W/V) POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER. THE QUINONOID INTERMEDIATE WITH 3-FLUORO-L-TYROSINE WAS PREPARED BY SOAKING THE TPL CRYSTALS FOR ABOUT 30 SECONDS IN THE STABILIZATION SOLUTION CONTAINING 40% POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER, 50 MM TRIETHANOLAMINE BUFFER (PH 8.0), 0.25 M KCL, 0.2 MM PLP, 0.5 MM DTT AND 10 MM 3-FLUORO-L-TYROSINE. CRYSTALS WERE FROZEN DIRECTLY FROM THE SOAKING SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: May 1, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 154478 / % possible obs: 99 % / Observed criterion σ(I): -10 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.5 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2EZ2 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.341 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.853 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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