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Yorodumi- PDB-6ecg: Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ecg | ||||||
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Title | Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-methionine | ||||||
Components | (Tyrosine phenol- ...) x 2 | ||||||
Keywords | LYASE / pyridoxal-5'-phosphate / aminotransferase fold | ||||||
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: 2.27 Å | ||||||
Authors | Phillips, R.S. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Authors: Phillips, R.S. / Craig, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ecg.cif.gz | 430.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ecg.ent.gz | 352.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ecg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ecg_validation.pdf.gz | 918.2 KB | Display | wwPDB validaton report |
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Full document | 6ecg_full_validation.pdf.gz | 929 KB | Display | |
Data in XML | 6ecg_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 6ecg_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6ecg ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ecg | HTTPS FTP |
-Related structure data
Related structure data | 6durC 6dvxC 6dxvC 6dytC 6dz5C 2vlhS 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
-Tyrosine phenol- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 51301.461 Da / Num. of mol.: 1 / Mutation: F448A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Plasmid: pLATE11-tpl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase |
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#2: Protein | Mass: 51529.578 Da / Num. of mol.: 1 / Mutation: F448A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Plasmid: pLATE11-tpl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase |
-Non-polymers , 5 types, 654 molecules
#3: Chemical | #4: Chemical | ChemComp-PM9 / ( | #5: Chemical | ChemComp-PGE / | #6: Chemical | ChemComp-P33 / | #7: 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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.05 M triethanolamine-HCl, pH 8.0, 0.2 M KCl, 1 mM DTT, 0.5 mM pyridoxal-5'-phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→45.95 Å / Num. obs: 53790 / % possible obs: 99.92 % / Redundancy: 6 % / Biso Wilson estimate: 42.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1189 / Rpim(I) all: 0.05322 / Rrim(I) all: 0.1307 / Net I/σ(I): 7.75 |
Reflection shell | Resolution: 2.27→2.351 Å / Redundancy: 6.2 % / Num. unique obs: 5280 / CC1/2: 0.239 / Rpim(I) all: 1.495 / Rrim(I) all: 3.751 / % possible all: 99.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VLH Resolution: 2.27→45.95 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→45.95 Å
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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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