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- PDB-7mdb: Crystal structure of Staphylococcus aureus cystathionine gamma ly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mdb | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103A mutant co-crystallized with NL2 | ||||||||||||
![]() | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 75.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7mcbC ![]() 7mclC ![]() 7mcnC ![]() 7mcpC ![]() 7mcqC ![]() 7mctC ![]() 7mcuC ![]() 7mcyC ![]() 7md0C ![]() 7md1C ![]() 7md6C ![]() 7md8C ![]() 7md9C ![]() 7mdaC ![]() 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: 41417.617 Da / Num. of mol.: 1 / Mutation: Y103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: X5E0F1, ![]() ![]() ![]() |
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-Non-polymers , 6 types, 361 molecules ![](data/chem/img/YXA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PLP / | ![]() #4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.76 Å3/Da / Density % sol: 74.18 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M sodium cacodylate , pH 6.5, 1.3 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![]() |
Reflection | Resolution: 1.8→30 Å / Num. obs: 74732 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 27.83 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.037 / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3667 / CC1/2: 0.748 / Rpim(I) all: 0.539 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4IXZ Resolution: 1.8→29.69 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5101 / 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: 32.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.69 Å
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Refine LS restraints |
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LS refinement shell |
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