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Yorodumi- PDB-7md1: Crystal structure of Staphylococcus aureus cystathionine gamma ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7md1 | ||||||||||||
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Title | Crystal structure of Staphylococcus aureus cystathionine gamma lyase holoenzyme Y103N mutant | ||||||||||||
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 gamma-synthase activity / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / : / cystathionine gamma-lyase activity / L-cysteine desulfhydrase activity / transsulfuration ...cystathionine gamma-synthase / cystathionine gamma-synthase activity (acts on O-phosphohomoserine) / cystathionine gamma-synthase activity / cystathionine beta-lyase / cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / : / 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: 2.3 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 | 7md1.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7md1.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 7md1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/7md1 ftp://data.pdbj.org/pub/pdb/validation_reports/md/7md1 | HTTPS FTP |
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-Related structure data
Related structure data | 7mcbC 7mclC 7mcnC 7mcpC 7mcqC 7mctC 7mcuC 7mcyC 7md0C 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: 41460.641 Da / Num. of mol.: 1 / Mutation: Y103N 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, 207 molecules
#2: Chemical | ChemComp-EPE / | ||||
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#3: Chemical | ChemComp-PLP / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium, pH 7.6, 1.2 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: 0.91956 Å |
Detector | Type: DECTRIS EIGER2 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: 2.3→30 Å / Num. obs: 36145 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.047 / Net I/σ(I): 61.3 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 2375 / CC1/2: 0.909 / Rpim(I) all: 0.417 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IXZ Resolution: 2.3→29.42 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9729 / 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: 41.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.42 Å
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Refine LS restraints |
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LS refinement shell |
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