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- PDB-5x2y: Crystal structure of Pseudomonas putida methionine gamma-lyase C1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x2y | ||||||
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Title | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant without sulfate ion | ||||||
![]() | L-methionine gamma-lyase | ||||||
![]() | LYASE / Pyridoxal 5'-phosphate | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Shiba, T. / Sato, D. / Harada, S. | ||||||
![]() | ![]() Title: Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis Authors: Sato, D. / Shiba, T. / Yunoto, S. / Furutani, K. / Fukumoto, M. / Kudou, D. / Tamura, T. / Inagaki, K. / Harada, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.4 KB | Display | ![]() |
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PDB format | ![]() | 251.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 491.3 KB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 87.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x2vC ![]() 5x2wC ![]() 5x2xC ![]() 5x2zC ![]() 5x30C ![]() 2o7cS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 42936.738 Da / Num. of mol.: 4 / Mutation: C116H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Na-K phosphate buffer, 6-10 % PEG 6000, 0.25 M ammonium sulfate. 0.5 mM PLP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 24, 2014 |
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: 1.79→50 Å / Num. obs: 180464 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.8 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O7C Resolution: 1.79→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.269 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.991 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→20 Å
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Refine LS restraints |
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