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Yorodumi- PDB-3jw9: Crystal structure of L-methionine gamma-lyase from Citrobacter fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jw9 | ||||||
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Title | Crystal structure of L-methionine gamma-lyase from Citrobacter freundii with S-ethyl-cysteine | ||||||
Components | Methionine gamma-lyase | ||||||
Keywords | LYASE / PYRIDOXAL-5'-PHOSPHATE / PLP-DEPENDENT ENZYME | ||||||
Function / homology | Function and homology information methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Citrobacter freundii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Revtovish, S.V. / Nikulin, A.D. / Morozova, E.A. / Demidkina, T.V. | ||||||
Citation | Journal: Biochemistry Mosc. / Year: 2011 Title: Three-dimensional structures of noncovalent complexes of Citrobacter freundii methionine gamma-lyase with substrates. Authors: Revtovich, S.V. / Morozova, E.A. / Khurs, E.N. / Zakomirdina, L.N. / Nikulin, A.D. / Demidkina, T.V. / Khomutov, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jw9.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jw9.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 3jw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jw9 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jw9 | HTTPS FTP |
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-Related structure data
Related structure data | 3jwaC 3jwbC 2rfvS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Details | THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE MONOMER IN THE ASYMMETRIC UNIT BY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION |
-Components
#1: Protein | Mass: 43164.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: megL / Plasmid: PET-MGL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84AR1, methionine gamma-lyase |
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#2: Chemical | ChemComp-ECX / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THERE IS AN ERROR IN THE DATABASE SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5% MMEPEG 2000, 50MM TRIS-HCl, 0.2MM PLP, 0.25% DTT , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 19, 2005 / Details: mirrors |
Radiation | Monochromator: Si(111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.843 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 40626 / Num. obs: 40626 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 18.83 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.63 / Num. unique all: 2977 / Rsym value: 0.342 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RFV Resolution: 1.8→20 Å / SU ML: 0.04 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.845 Å2 / ksol: 0.425 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell |
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