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Yorodumi- PDB-1cl2: CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cl2 | |||||||||
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Title | CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI IN COMPLEX WITH AMINOETHOXYVINYLGLYCINE | |||||||||
Components | CYSTATHIONINE BETA-LYASE | |||||||||
Keywords | METHIONINE BIOSYNTHESIS / PLP-DEPENDENT ENZYMES / C-S BETA LYASE / AMINOETHOXYVINYLGLYCINE / SLOW-BINDING INHIBITION | |||||||||
Function / homology | Function and homology information L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / alanine racemase activity / L-cysteine desulfhydrase activity / methionine biosynthetic process / transsulfuration / pyridoxal phosphate binding ...L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / : / alanine racemase activity / L-cysteine desulfhydrase activity / methionine biosynthetic process / transsulfuration / pyridoxal phosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | |||||||||
Authors | Clausen, T. / Huber, R. / Messerschmidt, A. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Slow-binding inhibition of Escherichia coli cystathionine beta-lyase by L-aminoethoxyvinylglycine: a kinetic and X-ray study. Authors: Clausen, T. / Huber, R. / Messerschmidt, A. / Pohlenz, H.D. / Laber, B. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cl2.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cl2.ent.gz | 169.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cl2 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cl2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.997, 0.001, -0.125), Vector: |
-Components
#1: Protein | Mass: 43261.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: METC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P06721, cystathionine beta-lyase #2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 40.84 % | ||||||||||||||||||||
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Crystal grow | pH: 8.2 / Details: 20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2) | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Laber, B., (1996) FEBS Lett., 379, 94. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.065 / Rsym value: 0.063 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 3.5 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Displacement parameters | Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |