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Yorodumi- PDB-2yct: Tyrosine phenol-lyase from Citrobacter freundii in complex with p... -
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-Basic information
Entry | Database: PDB / ID: 2yct | ||||||
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Title | Tyrosine phenol-lyase from Citrobacter freundii in complex with pyridine N-oxide and the quinonoid intermediate formed with L-alanine | ||||||
Components | TYROSINE PHENOL-LYASE | ||||||
Keywords | LYASE / PYRIDOXAL 5'-PHOSPHATE DEPENDENT ENZYME / BETA-ELIMINATION | ||||||
Function / homology | Function and homology information tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process Similarity search - Function | ||||||
Biological species | CITROBACTER FREUNDII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Milic, D. / Demidkina, T.V. / Faleev, N.G. / Phillips, R.S. / Matkovic-Calogovic, D. / Antson, A.A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yct.cif.gz | 383.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yct.ent.gz | 314.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yct_validation.pdf.gz | 950.5 KB | Display | wwPDB validaton report |
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Full document | 2yct_full_validation.pdf.gz | 958.2 KB | Display | |
Data in XML | 2yct_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 2yct_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2yct ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2yct | HTTPS FTP |
-Related structure data
Related structure data | 2ycnC 2ycpC 2ez2S C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51566.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Plasmid: PTZTPL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SVS 370 / References: UniProt: P31013, tyrosine phenol-lyase |
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-Non-polymers , 7 types, 801 molecules
#2: Chemical | #3: Chemical | ChemComp-PLI / ( | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-P33 / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | RESIDUE LYS 257 IN CHAIN A IS PARTIALLY MODIFIED BY COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 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) ...Details: CRYSTALS OF THE C. FREUNDII 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 50MM K-PHOSPHATE PH 8.0, 0.5 MM PLP, 1MM 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 ALANINE QUINONOID COMPLEX WITH PYRIDINE N-OXIDE (9PO) WAS PREPARED BY SOAKING WILD TYPE TPL CRYSTALS IN THE STABILIZATION SOLUTION CONTAINING 40% (W/V) POLY(ETHYLENE GLYCOL) 5000 MONOMETHYL ETHER (PEG 5000 MME), 50 MM TRIETHANOLAMINE PH 8.0, 0.25 M KCL, 0.2 MM PYRIDOXAL 5-PHOSPHATE (PLP), 0.5 MM DITHIOTHREITOL (DTT), WITH ADDITION OF 100 MM L- ALANINE AND A SATURATING CONCENTRATION OF PYRIDINE N-OXIDE. SINCE THE CRYSTALS QUALITY DETERIORATED RAPIDLY, THE SOAKING TIME WAS RESTRICTED TO ABOUT 20 S. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 55230 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.5 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EZ2 Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.823 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.16 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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