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- PDB-1gc0: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gc0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Motoshima, H. / Inagaki, K. / Kumasaka, T. / Furuichi, M. / Inoue, H. / Tamura, T. / Esaki, N. / Soda, K. / Tanaka, N. / Yamamoto, M. / Tanaka, H. | ||||||
![]() | ![]() Title: Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida. Authors: Motoshima, H. / Inagaki, K. / Kumasaka, T. / Furuichi, M. / Inoue, H. / Tamura, T. / Esaki, N. / Soda, K. / Tanaka, N. / Yamamoto, M. / Tanaka, H. #1: ![]() Title: Structural analysis of the L-methionine gamma-lyase gene from Pseudomonas putida. Authors: Inoue, H. / Inagaki, K. / Sugimoto, M. / Esaki, N. / Soda, K. / Tanaka, H. #2: ![]() Title: Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A. Authors: Clausen, T. / Huber, R. / Laber, B. / Pohlenz, H.D. / Messerschmidt, A. #3: ![]() Title: Crystal structure of Escherichia coli cystathionine gamma-synthase at 1.5 A resolution. Authors: Clausen, T. / Huber, R. / Prade, L. / Wahl, M.C. / Messerschmidt, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.9 KB | Display | ![]() |
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PDB format | ![]() | 239.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 500.4 KB | Display | |
Data in XML | ![]() | 70.1 KB | Display | |
Data in CIF | ![]() | 99.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 42901.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å / Num. all: 263490 / Num. obs: 144898 / % possible obs: 90.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 28.5 |
Reflection | *PLUS Rmerge(I) obs: 0.037 |
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Processing
Software | Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→71.46 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1463068.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.95 Å2 / ksol: 0.381 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→71.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.211 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / Rfactor Rwork: 0.239 / Rfactor obs: 0.239 |