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Yorodumi- PDB-5x2x: Crystal structure of Pseudomonas putida methionine gamma-lyase wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x2x | ||||||
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Title | Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates | ||||||
Components | L-methionine gamma-lyase | ||||||
Keywords | LYASE / Pyridoxal 5'-phosphate | ||||||
Function / homology | Function and homology information homocysteine desulfhydrase / homocysteine desulfhydrase activity / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shiba, T. / Sato, D. / Harada, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x2x.cif.gz | 305.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x2x.ent.gz | 247.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/5x2x ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x2x | HTTPS FTP |
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-Related structure data
Related structure data | 5x2vC 5x2wC 5x2yC 5x2zC 5x30C 2o7cS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 42673.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdeA / Production host: Escherichia coli (E. coli) References: UniProt: P13254, methionine gamma-lyase, homocysteine desulfhydrase #2: Chemical | ChemComp-4LM / ( #3: Chemical | ChemComp-H2S / #4: 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: 2.79 Å3/Da / Density % sol: 55.86 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 25, 2016 |
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→50 Å / Num. obs: 129275 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.614 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O7C Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.454 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.137 / 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: 30.425 Å2
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Refinement step | Cycle: 1 / Resolution: 2→20 Å
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Refine LS restraints |
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