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Yorodumi- PDB-2vlf: Quinonoid intermediate of Citrobacter freundii tyrosine phenol-ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vlf | ||||||
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Title | Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with alanine | ||||||
Components | TYROSINE PHENOL-LYASE | ||||||
Keywords | LYASE / PLP-DEPENDENT ENZYME / TYROSINE DEGRADATION | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Milic, D. / Demidkina, T.V. / Matkovic-Calogovic, D. / Antson, A.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Insights Into the Catalytic Mechanism of Tyrosine Phenol-Lyase from X-Ray Structures of Quinonoid Intermediates. Authors: Milic, D. / Demidkina, T.V. / Faleev, N.G. / 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 | 2vlf.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vlf.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vlf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2vlf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2vlf_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2vlf_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vlf ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vlf | HTTPS FTP |
-Related structure data
Related structure data | 2vlhC 2ez2S 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 on special symmetry positions |
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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 , 5 types, 972 molecules
#2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | #5: Chemical | ChemComp-P33 / | #6: Water | ChemComp-HOH / | |
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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: 2.76 Å3/Da / Density % sol: 55.5 % / 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. QUINONOID INTERMEDIATE WITH ALANINE WAS PREPARED BY SOAKING THE TPL CRYSTALS FOR 5 MIN 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 L-ALA. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.862 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 7, 1995 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.862 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→20 Å / Num. obs: 89055 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.36 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EZ2 Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.252 / SU ML: 0.083 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.118 / 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: 22.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
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Refine LS restraints |
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