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Yorodumi- PDB-2d4u: Crystal Structure of the ligand binding domain of the bacterial s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d4u | ||||||
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Title | Crystal Structure of the ligand binding domain of the bacterial serine chemoreceptor Tsr | ||||||
Components | Methyl-accepting chemotaxis protein I | ||||||
Keywords | SIGNALING PROTEIN / helix-turn-helix | ||||||
Function / homology | Function and homology information regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / transmembrane signaling receptor activity ...regulation of protein histidine kinase activity / detection of chemical stimulus / methyl accepting chemotaxis protein complex / regulation of bacterial-type flagellum-dependent cell motility / regulation of chemotaxis / signal complex assembly / receptor clustering / cell motility / cellular response to amino acid stimulus / transmembrane signaling receptor activity / chemotaxis / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Imada, K. / Tajima, H. / Namba, K. / Sakuma, M. / Homma, M. / Kawagishi, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Ligand specificity determined by differentially arranged common ligand-binding residues in the bacterial amino acid chemoreceptors Tsr and Tar. Authors: Tajima, H. / Imada, K. / Sakuma, M. / Hattori, F. / Nara, T. / Kamo, N. / Homma, M. / Kawagishi, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d4u.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4u.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2d4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4u ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4u | HTTPS FTP |
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-Related structure data
Related structure data | 3atpC 2ligS 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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Details | The biological assmbly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 19836.902 Da / Num. of mol.: 2 / Fragment: ligand binding domain / Mutation: D36S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02942 #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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 15-20% PEG 10000, 0.1M Tris HCl, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 35 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2005 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→43.85 Å / Num. all: 24764 / Num. obs: 24467 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 5.9 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2lig Resolution: 1.95→43.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.038 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.558 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→43.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20 /
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