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- PDB-7md6: Crystal structure of Staphylococcus aureus cystathionine gamma ly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7md6 | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N mutant co-crystallized with NL1 | ||||||||||||
![]() | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||||||||
![]() | LYASE / Amino-acid biosynthesis / Cysteine biosynthesis / Hydrogen sulfide production / PLP dependent enzyme | ||||||||||||
Function / homology | ![]() cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine beta-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / : / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration ...cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine beta-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / : / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Nuthanakanti, A. / Serganov, A. / Kaushik, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors of bacterial H 2 S biogenesis targeting antibiotic resistance and tolerance. Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / ...Authors: Shatalin, K. / Nuthanakanti, A. / Kaushik, A. / Shishov, D. / Peselis, A. / Shamovsky, I. / Pani, B. / Lechpammer, M. / Vasilyev, N. / Shatalina, E. / Rebatchouk, D. / Mironov, A. / Fedichev, P. / Serganov, A. / Nudler, E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mcbC ![]() 7mclC ![]() 7mcnC ![]() 7mcpC ![]() 7mcqC ![]() 7mctC ![]() 7mcuC ![]() 7mcyC ![]() 7md0C ![]() 7md1C ![]() 7md8C ![]() 7md9C ![]() 7mdaC ![]() 7mdbC ![]() 4ixzS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 41460.641 Da / Num. of mol.: 1 / Mutation: Y103N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: X5E0F1, cystathionine gamma-lyase, cystathionine beta-lyase, cystathionine gamma-synthase | ||||||||
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#2: Chemical | ChemComp-LB6 / #3: Chemical | ChemComp-FLC / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 73.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 0.1 M Tris-HCl, pH 7.6, 1.2 M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91956 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 40858 / % possible obs: 99.9 % / Redundancy: 16.4 % / Biso Wilson estimate: 35.87 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.047 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.131 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2213 / CC1/2: 0.833 / Rpim(I) all: 0.339 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4IXZ Resolution: 2.2→29.77 Å / SU ML: 0.2192 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.769 / Stereochemistry target values: CDL v1.2
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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 mean: 41.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29.77 Å
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Refine LS restraints |
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LS refinement shell |
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