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Yorodumi- PDB-4yn8: Crystal Structure of Response Regulator ChrA in Heme-Sensing Two ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yn8 | ||||||||||||
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Title | Crystal Structure of Response Regulator ChrA in Heme-Sensing Two Component System | ||||||||||||
Components | Response regulator ChrA | ||||||||||||
Keywords | DNA BINDING PROTEIN / DNA-binding / helix-turn-helix | ||||||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Doi, A. / Nakamura, H. / Shiro, Y. / Sugimoto, H. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae. Authors: Doi, A. / Nakamura, H. / Shiro, Y. / Sugimoto, H. #1: Journal: FEBS Lett. / Year: 2009 Title: Heme-dependent autophosphorylation of a heme sensor kinase, ChrS, from Corynebacterium diphtheriae reconstituted in proteoliposomes. Authors: Ito, Y. / Nakagawa, S. / Komagata, A. / Ikeda-Saito, M. / Shiro, Y. / Nakamura, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yn8.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yn8.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yn8_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 4yn8_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 4yn8_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4yn8_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/4yn8 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/4yn8 | HTTPS FTP |
-Related structure data
Related structure data | 3eulS 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: 21638.705 Da / Num. of mol.: 1 / Mutation: M1S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: chrA / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RPE9 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M magnesium sulfate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2012 / Details: mirrors |
Diffraction measurement | Details: 1.00 degrees, 1.8 sec, detector distance 140.00 mm |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.096 / Number: 404586 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 28694 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 30.035 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 7.843 / Rsym value: 0.418 / % possible all: 97 |
Cell measurement | Reflection used: 404586 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EUL Resolution: 1.8→28.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1997 / WRfactor Rwork: 0.1766 / FOM work R set: 0.8863 / SU B: 1.736 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0972 / SU Rfree: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.01 Å2 / Biso mean: 16.295 Å2 / Biso min: 5.31 Å2
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Refinement step | Cycle: final / Resolution: 1.8→28.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.843 Å / Total num. of bins used: 20
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