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Yorodumi- PDB-5wbf: Double CACHE (dCACHE) sensing domain of TlpC chemoreceptor from H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wbf | |||||||||
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Title | Double CACHE (dCACHE) sensing domain of TlpC chemoreceptor from Helicobacter pylori | |||||||||
Components | Methyl-accepting chemotaxis transducer (TlpC) | |||||||||
Keywords | SIGNALING PROTEIN / Bacterial protein / Chemoreceptor sensing domain / double-CACHE domain / Helicobacter pylori | |||||||||
Function / homology | Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / membrane => GO:0016020 / signal transduction / LACTIC ACID / Methyl-accepting chemotaxis transducer (TlpC) Function and homology information | |||||||||
Biological species | Helicobacter pylori (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.19 Å | |||||||||
Authors | Machuca, M.A. / Johnson, K.S. / Liu, Y.C. / Steer, D.L. / Ottemann, K.M. / Roujeinikova, A. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate. Authors: Machuca, M.A. / Johnson, K.S. / Liu, Y.C. / Steer, D.L. / Ottemann, K.M. / Roujeinikova, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wbf.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wbf.ent.gz | 141.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wbf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5wbf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5wbf_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 5wbf_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/5wbf ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wbf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30602.799 Da / Num. of mol.: 3 Fragment: Double CACHE (dCACHE) sensing domain (UNP residues 34-297) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O24911 #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M MgCl2, 0.1 M MES/NaOH (pH 6.5), 22% (w/v) PEG 4000 and 10 mM BaCl2H4O2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.5498 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5498 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→30.57 Å / Num. obs: 59028 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.038 / Rrim(I) all: 0.073 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.19→30.57 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.19→30.57 Å
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LS refinement shell | Resolution: 2.19→2.31 Å |