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Yorodumi- PDB-4jgr: The crystal structure of sporulation kinase D mutant sensor domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jgr | |||||||||
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Title | The crystal structure of sporulation kinase D mutant sensor domain, R131A, from Bacillus subtilis subsp at 2.4A resolution | |||||||||
Components | Sporulation kinase D | |||||||||
Keywords | TRANSFERASE / PAS-like fold / Histidine kinase / Extracytoplasmic / alpha-beta-alpha structure / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology | |||||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | |||||||||
Authors | Wu, R. / Schiffer, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Authors: Wu, R. / Gu, M. / Wilton, R. / Babnigg, G. / Kim, Y. / Pokkuluri, P.R. / Szurmant, H. / Joachimiak, A. / Schiffer, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jgr.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jgr.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jgr_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 4jgr_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 4jgr_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4jgr_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/4jgr ftp://data.pdbj.org/pub/pdb/validation_reports/jg/4jgr | HTTPS FTP |
-Related structure data
Related structure data | 4jgoC 4jgpC 4jgqC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24490.166 Da / Num. of mol.: 2 / Fragment: SENSOR DOMAIN (UNP RESIDUES 37-250) / Mutation: R95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU13660, kinD, ykvD / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: O31671, histidine kinase #2: Chemical | #3: Chemical | #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: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M AMMONIUM ACETATE, 0.1M BIS-TRIS AND 25% (W/V) PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI 111, CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 23104 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.088 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.61 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→37.92 Å / SU ML: 0.97 / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.49 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→37.92 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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