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Yorodumi- PDB-1gc2: CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gc2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE PYRIDOXAL-5'-PHOSPHATE DEPENDENT L-METHIONINE GAMMA-LYASE FROM PSEUDOMONAS PUTIDA | ||||||
Components | 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 / Resolution: 2 Å | ||||||
Authors | Motoshima, H. / Inagaki, K. / Kumasaka, T. / Furuichi, M. / Inoue, H. / Tamura, T. / Esaki, N. / Soda, K. / Tanaka, N. / Yamamoto, M. / Tanaka, H. | ||||||
Citation | Journal: J.Biochem. / Year: 2000 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: Journal: J.BIOCHEM.(TOKYO) / Year: 1995 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: Journal: J.Mol.Biol. / Year: 1996 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: Journal: Embo J. / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gc2.cif.gz | 307.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gc2.ent.gz | 248.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gc2 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gc2 | HTTPS FTP |
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-Related 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: 42901.734 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: P13254, methionine gamma-lyase #2: 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: 2.78 Å3/Da / Density % sol: 55.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Highest resolution: 1.7 Å / Num. all: 1016993 / Num. obs: 130168 / % possible obs: 99.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9 | ||||||||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 1016993 / Rmerge(I) obs: 0.079 |
-Processing
Software |
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Refinement | Resolution: 2→83.43 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 320661.45 / 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: 65.34 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→83.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.211 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.297 / Rfactor Rwork: 0.268 / Rfactor obs: 0.268 |