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Yorodumi- PDB-3gl9: The structure of a histidine kinase-response regulator complex sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gl9 | ||||||
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Title | The structure of a histidine kinase-response regulator complex sheds light into two-component signaling and reveals a novel cis autophosphorylation mechanism | ||||||
Components | Response regulator | ||||||
Keywords | SIGNALING PROTEIN / beta-sheet / surrounded by alpha helices / both sides | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Casino, P. / Rubio, V. / Marina, A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction Authors: Casino, P. / Rubio, V. / Marina, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gl9.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gl9.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/3gl9 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/3gl9 | HTTPS FTP |
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-Related structure data
Related structure data | 3dgeSC 3dgfC 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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Unit cell |
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-Components
#1: Protein | Mass: 13913.255 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET21d / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9WYT9 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #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: 2.16 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.9M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2008 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horiz. foc. by sagittal curved 2nd crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→29.3 Å / Num. obs: 44647 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.33 / Net I/σ(I): 7.083 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DGE Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.874 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.148 / ESU R Free: 0.143 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.14 Å2 / Biso mean: 16.99 Å2 / Biso min: 3.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 20
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