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Yorodumi- PDB-6o5c: X-ray crystal structure of metal-dependent transcriptional regula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o5c | ||||||
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Title | X-ray crystal structure of metal-dependent transcriptional regulator MtsR | ||||||
Components | Putative metal-dependent transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN / Manganese / Transcription Regulator | ||||||
Function / homology | Function and homology information transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes serotype M3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Do, H. / Kumaraswami, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Metal sensing and regulation of adaptive responses to manganese limitation by MtsR is critical for group A streptococcus virulence. Authors: Do, H. / Makthal, N. / Chandrangsu, P. / Olsen, R.J. / Helmann, J.D. / Musser, J.M. / Kumaraswami, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o5c.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o5c.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/6o5c ftp://data.pdbj.org/pub/pdb/validation_reports/o5/6o5c | HTTPS FTP |
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-Related structure data
Related structure data | 5cviS S: Starting model for refinement |
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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
#1: Protein | Mass: 25198.986 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UTK0 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
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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: 3.36 Å3/Da / Density % sol: 63.38 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40 mM sodium acetate, 0.16 M magnesium formate, 2.6 M lithium acetate, 20% PEG 2000, 66 mM ammonium sulfate, and 0.8 mM manganese chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 23865 / % possible obs: 99.8 % / Redundancy: 6.1 % / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.1→3.27 Å / Num. unique obs: 3461 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CVI Resolution: 3.1→29.738 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→29.738 Å
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Refine LS restraints |
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LS refinement shell |
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