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- PDB-7f1u: Crystal structure of Pseudomonas putida methionine gamma-lyase Q3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f1u | ||||||
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Title | Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediates | ||||||
![]() | (L-methionine gamma-lyase) x 2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K. | ||||||
![]() | ![]() Title: Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine. Authors: Okawa, A. / Handa, H. / Yasuda, E. / Murota, M. / Kudo, D. / Tamura, T. / Shiba, T. / Inagaki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302 KB | Display | ![]() |
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PDB format | ![]() | 243.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7f1pC ![]() 7f1vC ![]() 2o7cS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42632.566 Da / Num. of mol.: 3 / Mutation: Q349S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P13254, ![]() ![]() #2: Protein | | Mass: 42860.684 Da / Num. of mol.: 1 / Mutation: Q349S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P13254, ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-MET / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.77 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M NA-K PHOSPHATE BUFFER, pH 5.6-5.8, 6-9 % PEG 6000, 0.25 M AMMONIUM SULFATE. 0.5 MM PLP, 0.5%(v/v) 2-mercaptoethanol PH range: 5.6-5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 19, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→50 Å / Num. obs: 74230 / % possible obs: 98.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3415 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2O7C Resolution: 2.4→19.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.716 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.242 / 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: 42.632 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→19.93 Å
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Refine LS restraints |
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