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- PDB-7md8: Crystal structure of Staphylococcus aureus cystathionine gamma ly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7md8 | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N mutant co-crystallized with NL2 | ||||||||||||
![]() | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||||||||
![]() | LYASE / Amino-acid biosynthesis / Cysteine biosynthesis / Hydrogen sulfide production / PLP dependent enzyme | ||||||||||||
Function / homology | ![]() cystathionine gamma-synthase / : / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding ...cystathionine gamma-synthase / : / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-synthase activity / 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 | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7mcbC ![]() 7mclC ![]() 7mcnC ![]() 7mcpC ![]() 7mcqC ![]() 7mctC ![]() 7mcuC ![]() 7mcyC ![]() 7md0C ![]() 7md1C ![]() 7md6C ![]() 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
-Protein , 1 types, 1 molecules H
#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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-Non-polymers , 5 types, 269 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.88 Å3/Da / Density % sol: 74.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium, pH 7.5, 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: 2.06→30 Å / Num. obs: 51126 / % possible obs: 100 % / Redundancy: 16 % / Biso Wilson estimate: 33.98 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.262 / Rpim(I) all: 0.066 / Net I/σ(I): 76.8 |
Reflection shell | Resolution: 2.06→2.1 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.972 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 3135 / CC1/2: 0.485 / Rpim(I) all: 0.587 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4IXZ Resolution: 2.06→29.76 Å / SU ML: 0.263 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0866 / 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: 38.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→29.76 Å
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Refine LS restraints |
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LS refinement shell |
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