[English] 日本語
Yorodumi- PDB-7mcy: Crystal structure of Staphylococcus aureus Cystathionine gamma ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mcy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with bound NL3 | ||||||||||||
Components | Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase | ||||||||||||
Keywords | LYASE / Amino-acid biosynthesis / Cysteine biosynthesis / Hydrogen sulfide production / PLP dependent enzyme | ||||||||||||
Function / homology | Function and homology information cystathionine gamma-synthase / : / 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 Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||||||||
Authors | Nuthanakanti, A. / Serganov, A. / Kaushik, A. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Science / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mcy.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mcy.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 7mcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mcy_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mcy_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7mcy_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 7mcy_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/7mcy ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mcy | HTTPS FTP |
-Related structure data
Related structure data | 7mcbC 7mclC 7mcnC 7mcpC 7mcqC 7mctC 7mcuC 7md0C 7md1C 7md6C 7md8C 7md9C 7mdaC 7mdbC 4ixzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-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.) Staphylococcus aureus (bacteria) / Gene: mccB / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: X5E0F1, cystathionine gamma-lyase, cystathionine beta-lyase, cystathionine gamma-synthase |
---|
-Non-polymers , 6 types, 460 molecules
#2: Chemical | ChemComp-PLP / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-EPE / | ||||
#4: Chemical | ChemComp-NL3 / | ||||
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.47 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris-HCl, pH 7.5, 1.4 M Tri Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92013 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92013 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→30 Å / Num. obs: 85730 / % possible obs: 99.4 % / Redundancy: 14.4 % / Biso Wilson estimate: 19.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.031 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3829 / CC1/2: 0.826 / Rpim(I) all: 0.288 / % possible all: 89.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IXZ Resolution: 1.72→29.71 Å / SU ML: 0.2097 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6286 / Stereochemistry target values: CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→29.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|