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- PDB-7mcn: Crystal structure of Staphylococcus aureus Cystathionine gamma-ly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mcn | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus Cystathionine gamma-lyase, Holoenzyme with High HEPES | ||||||||||||
![]() | 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 | ![]() | 113.3 KB | Display | ![]() |
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PDB format | ![]() | 69.4 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 ![]() 7mcpC ![]() 7mcqC ![]() 7mctC ![]() 7mcuC ![]() 7mcyC ![]() 7md0C ![]() 7md1C ![]() 7md6C ![]() 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
-Protein , 1 types, 1 molecules H
#1: Protein | Mass: 41509.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: X5E0F1, ![]() ![]() ![]() |
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-Non-polymers , 5 types, 164 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PLP / ![]() | ||||
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#3: Chemical | ChemComp-EPE / ![]() | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / ![]() #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: 4.71 Å3/Da / Density % sol: 73.89 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES-Na, pH 7.5, 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 EIGER2 X 9M / Detector: PIXEL / Date: Nov 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.52→30 Å / Num. obs: 27451 / % possible obs: 99.8 % / Redundancy: 22.6 % / Biso Wilson estimate: 40.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.033 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.52→2.58 Å / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 4 / Num. unique obs: 1944 / CC1/2: 0.979 / Rpim(I) all: 0.211 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4IXZ Resolution: 2.52→29.6 Å / SU ML: 0.2011 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2426 / 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: 45.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→29.6 Å
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Refine LS restraints |
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LS refinement shell |
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