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Yorodumi- PDB-5u8m: A novel family of redox sensors in the streptococci evolved from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u8m | ||||||
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Title | A novel family of redox sensors in the streptococci evolved from two-component response regulators | ||||||
Components | Response regulator | ||||||
Keywords | TRANSCRIPTION / Repressor of iron transporter / Aspartate-less receiver domain protein / transcription regulator / cross-dimer | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å | ||||||
Authors | Han, L. / Silvaggi, N.R. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2018 Title: RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization. Authors: Glanville, D.G. / Han, L. / Maule, A.F. / Woodacre, A. / Thanki, D. / Abdullah, I.T. / Morrissey, J.A. / Clarke, T.B. / Yesilkaya, H. / Silvaggi, N.R. / Ulijasz, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u8m.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u8m.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 5u8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u8m_validation.pdf.gz | 432.7 KB | Display | wwPDB validaton report |
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Full document | 5u8m_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 5u8m_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5u8m_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/5u8m ftp://data.pdbj.org/pub/pdb/validation_reports/u8/5u8m | HTTPS FTP |
-Related structure data
Related structure data | 5u8kSC 5vfaC 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
#1: Protein | Mass: 27032.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain Hungary19A-6) (bacteria) Strain: Hungary19A-6 / Gene: SPH_0483 / Plasmid: pE-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1I9H6 #2: 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: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.3 M Magnesium sulfate, 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 64031 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.5 / Num. unique all: 24543 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U8K Resolution: 2.105→42.368 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.77 / Phase error: 27.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.105→42.368 Å
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Refine LS restraints |
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LS refinement shell |
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