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- PDB-8bis: Crystal structure of cystathionine gamma-lyase from Toxoplasma go... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bis | |||||||||||||||||||||
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Title | Crystal structure of cystathionine gamma-lyase from Toxoplasma gondii in complex with DL-propargylglycine | |||||||||||||||||||||
![]() | Cystathionine beta-lyase, putative | |||||||||||||||||||||
![]() | CYTOSOLIC PROTEIN / transsulfuration pathway / hydrogen sulfide / propargylglgycine / cystathionine gamma-lyase | |||||||||||||||||||||
Function / homology | ![]() cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Fernandez-Rodriguez, C. / Conter, C. / Oyenarte, I. / Favretto, F. / Quintana, I. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis of the inhibition of cystathionine gamma-lyase from Toxoplasma gondii by propargylglycine and cysteine. Authors: Fernandez-Rodriguez, C. / Conter, C. / Oyenarte, I. / Favretto, F. / Quintana, I. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.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 | ![]() | 168.6 KB | Display | ![]() |
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PDB format | ![]() | 132.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7nl1C ![]() 8biuC ![]() 8bivC ![]() 8biwC ![]() 8bixC ![]() 8bizC ![]() 2nmpS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45981.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-2AG / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 12% (w/v) PEG 3350, 0.1 M sodium citrate pH 4.6, CYMAL-4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→45.452 Å / Num. obs: 61247 / % possible obs: 98.8 % / Redundancy: 26.8 % / CC1/2: 0.995 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.26→2.31 Å / Num. unique obs: 2656 / CC1/2: 0.641 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NMP Resolution: 2.266→45.452 Å / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.266→45.452 Å
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Refine LS restraints |
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LS refinement shell |
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