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- PDB-3vk4: Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas pu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vk4 | ||||||
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Title | Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine | ||||||
![]() | Methionine gamma-lyase | ||||||
![]() | LYASE / PLP-dependent enzyme / PLP | ||||||
Function / homology | ![]() homocysteine desulfhydrase / homocysteine desulfhydrase activity / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukumoto, M. / Kudou, D. / Murano, S. / Shiba, T. / Sato, D. / Tamura, T. / Harada, S. / Inagaki, K. | ||||||
![]() | ![]() Title: The role of amino acid residues in the active site of L-methionine gamma-lyase from Pseudomonas putida. Authors: Fukumoto, M. / Kudou, D. / Murano, S. / Shiba, T. / Sato, D. / Tamura, T. / Harada, S. / 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 | ![]() | 296.7 KB | Display | ![]() |
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PDB format | ![]() | 243 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vk2C ![]() 3vk3C ![]() 2o7cS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42936.738 Da / Num. of mol.: 4 / Mutation: C116H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HCS / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 12.5% PEG6000, 0.25M ammonium sulfate, 0.2M MES, 0.5mM PLP, 0.5% 2-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 17, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 57780 / Num. obs: 57379 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.149 / Rsym value: 0.067 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2O7C Resolution: 2.61→29.28 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 10.481 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.695 / ESU R Free: 0.318 / 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: 29.487 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→29.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.613→2.68 Å / Total num. of bins used: 20
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