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- PDB-5x30: 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: 5x30 | ||||||
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Title | Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates. | ||||||
![]() | (L-methionine gamma- ...) x 2 | ||||||
![]() | 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 | ![]() | 325.8 KB | Display | ![]() |
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PDB format | ![]() | 262.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 67 KB | Display | |
Data in CIF | ![]() | 95.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x2vC ![]() 5x2wC ![]() 5x2xC ![]() 5x2yC ![]() 5x2zC ![]() 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
-L-methionine gamma- ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 42936.738 Da / Num. of mol.: 2 / Mutation: C116H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase #2: Protein | Mass: 42708.621 Da / Num. of mol.: 2 / Mutation: C116H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase |
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-Non-polymers , 5 types, 1026 molecules ![](data/chem/img/HCS.gif)
![](data/chem/img/4LM.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/7XF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4LM.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/7XF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-4LM / ( | #5: Chemical | ChemComp-H2S / | #6: Chemical | ChemComp-7XF / ( | #7: 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, hanging drop Details: 0.2M Na-K phosphate buffer, 6-10% PEG 6000, 0.25M ammonium sulfate. 0.5mM PLP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 4, 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: 1.7→50 Å / Num. obs: 208507 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O7C Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.817 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / 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: 29.41 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→20 Å
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Refine LS restraints |
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