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Yorodumi- PDB-1e5e: METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e5e | ||||||
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Title | METHIONINE GAMMA-LYASE (MGL) FROM TRICHOMONAS VAGINALIS IN COMPLEX WITH PROPARGYLGLYCINE | ||||||
Components | METHIONINE GAMMA-LYASE | ||||||
Keywords | LYASE / METHIONINE BIOSYNTHESIS / PLP-DEPENDENT ENZYMES / C-S GAMMA LYASE | ||||||
Function / homology | Function and homology information carbon-sulfur lyase activity / methionine gamma-lyase / methionine gamma-lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | TRICHOMONAS VAGINALIS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Goodall, G. / Mottram, J.C. / Coombs, G.H. / Lapthorn, A.J. | ||||||
Citation | Journal: To be Published Title: The Structure and Proposed Catalytic Mechanism of Methionine Gamma-Lyase Authors: Goodall, G. / Mottram, J.C. / Coombs, G.H. / Lapthorn, A.J. #1: Journal: J.Biol.Chem. / Year: 1998 Title: The Primitive Protozoon Trichomonas Vaginalis Contains Two Methionine Gamma-Lyase Genes that Encode Members of the Gamma Family of Pyridoxal 5'-Phosphate Enzymes Authors: Mckie, A.E. / Edlind, T. / Walker, J. / Mottram, J.C. / Coombs, G.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e5e.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e5e.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/1e5e ftp://data.pdbj.org/pub/pdb/validation_reports/e5/1e5e | HTTPS FTP |
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-Related structure data
Related structure data | 1e5fC 1cl1S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.67872, -0.00427, -0.73439), Vector: |
-Components
#1: Protein | Mass: 44149.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN PROPARGYLGLYCINE AND TYR 111 / Source: (gene. exp.) TRICHOMONAS VAGINALIS (eukaryote) / Strain: G3 / Cellular location: CYTOPLASM / Gene: MGL1 / Plasmid: PQE60 / Production host: ESCHERICHIA COLI M15 (bacteria) References: UniProt: O15564, UniProt: A2FEV4*PLUS, methionine gamma-lyase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CHAIN A,B: SOME CHANGES TO SEQUENCE INTRODUCED | |
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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: 2.85 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | pH: 5.6 Details: 3.2M AMMONIUM SULPHATE, 0.2M LISO4, 0.1M CITRATE PH5.6, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
Radiation | Monochromator: SI 111 CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→28.9 Å / Num. obs: 48724 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.05 / Rsym value: 0.196 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CL1 Resolution: 2.18→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.168
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Displacement parameters | Biso mean: 24.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→25 Å
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Refine LS restraints |
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