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- PDB-1ibj: Crystal structure of cystathionine beta-lyase from Arabidopsis th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ibj | ||||||
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Title | Crystal structure of cystathionine beta-lyase from Arabidopsis thaliana | ||||||
![]() | CYSTATHIONINE BETA-LYASE | ||||||
![]() | LYASE / PLP-dependent enzyme / Methionine biosynthesis / Transsulfuration | ||||||
Function / homology | ![]() L-methionine biosynthetic process from L-homoserine via cystathionine / cysteine-S-conjugate beta-lyase activity / carbon-sulfur lyase activity / cysteine-S-conjugate beta-lyase / : / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / chloroplast stroma / chloroplast ...L-methionine biosynthetic process from L-homoserine via cystathionine / cysteine-S-conjugate beta-lyase activity / carbon-sulfur lyase activity / cysteine-S-conjugate beta-lyase / : / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / chloroplast stroma / chloroplast / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Breitinger, U. / Clausen, T. / Messerschmidt, A. | ||||||
![]() | ![]() Title: The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity Authors: Breitinger, U. / Clausen, T. / Ehlert, S. / Huber, R. / Laber, B. / Schmidt, F. / Pohl, E. / 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 | ![]() | 161.7 KB | Display | ![]() |
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PDB format | ![]() | 126.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.3 KB | Display | ![]() |
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Full document | ![]() | 518.5 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qgnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | Two active dimers, related by 2-fold crystallographic symmetry, form the homotetramer. |
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Components
#1: Protein | Mass: 50490.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Ammonium sulfate, Mes-NaOH, PLP, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1999 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. all: 108362 / Num. obs: 102185 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.072 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.1 / Num. unique all: 39111 / Rsym value: 0.141 / % possible all: 81.6 |
Reflection | *PLUS Num. obs: 37727 / Num. measured all: 102185 |
Reflection shell | *PLUS % possible obs: 81.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QGN Resolution: 2.3→6 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.309 / Rfactor Rwork: 0.249 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |