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- PDB-7nl1: Crystal structure of cystathionine gamma-lyase from Toxoplasma gondii -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nl1 | |||||||||
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Title | Crystal structure of cystathionine gamma-lyase from Toxoplasma gondii | |||||||||
![]() | Cystathione gamma lyase, putative | |||||||||
![]() | CYTOSOLIC PROTEIN / transsulfuration pathway / cysteine / hydrogen sulfide / PLP dependent | |||||||||
Function / homology | ![]() cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fernandez-Rodriguez, C. / Conter, C. / Recio, I. / 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bisC ![]() 8biuC ![]() 8bivC ![]() 8biwC ![]() 8bixC ![]() 8bizC ![]() 2nmpS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45981.520 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 50611 / Me49 / Gene: TGME49_312930 / Production host: ![]() ![]() #2: Chemical | ChemComp-PLP / #3: 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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 12% PEG 3350, 0.1M sodium citrate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.331→48.446 Å / Num. obs: 177123 / % possible obs: 100 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.036 / Rrim(I) all: 0.157 / Net I/σ(I): 19 / Num. measured all: 3461898 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2NMP Resolution: 2.331→48.446 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.11 Å2 / Biso mean: 51.2084 Å2 / Biso min: 26.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.331→48.446 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 12.1136 Å / Origin y: 33.8973 Å / Origin z: 57.4558 Å
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Refinement TLS group |
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