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Yorodumi- PDB-7mct: Crystal structure of Staphylococcus aureus Cystathionine gamma ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mct | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus Cystathionine gamma lyase, Holoenzyme with bound NL1 | ||||||||||||
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 gamma-synthase activity (acts on O-phosphohomoserine) / 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 ...cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / 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 | Staphylococcus aureus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Nuthanakanti, A. / Serganov, A. / Kaushik, A. | ||||||||||||
Funding support | United States, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mct.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mct.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mct_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7mct_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7mct_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 7mct_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/7mct ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mct | HTTPS FTP |
-Related structure data
Related structure data | 7mcbC 7mclC 7mcnC 7mcpC 7mcqC 7mcuC 7mcyC 7md0C 7md1C 7md6C 7md8C 7md9C 7mdaC 7mdbC 4ixzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Staphylococcus aureus (bacteria) / Gene: mccB / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: X5E0F1, cystathionine gamma-lyase, cystathionine beta-lyase, cystathionine gamma-synthase |
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-Non-polymers , 5 types, 461 molecules
#2: Chemical | ChemComp-LB6 / #3: Chemical | ChemComp-PLP / | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Nonpolymer details | LB6 molecule was used during co-crystallization, however in some places authors were able to see ...LB6 molecule was used during co-crystallization, however in some places authors were able to see only bromine atoms. Atom positions are assigned based on bromine anomalous signal while the rest of the LB6 molecule is disordered. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density % sol: 74.34 % |
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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, 1.4 M Tri Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9189 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9189 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 106360 / % possible obs: 99.6 % / Redundancy: 22.1 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.025 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 19.4 % / Rmerge(I) obs: 2.558 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7458 / CC1/2: 0.803 / Rpim(I) all: 0.585 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IXZ Resolution: 1.6→29.71 Å / SU ML: 0.1566 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.6248 / 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: 29.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→29.71 Å
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Refine LS restraints |
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LS refinement shell |
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