[English] 日本語
Yorodumi- PDB-6w3t: Crystal structure of ligand-binding domain of Campylobacter jejun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w3t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with L-norvaline | ||||||
Components | Methyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins | ||||||
Keywords | SIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain | ||||||
Function / homology | Function and homology information chemotaxis / membrane => GO:0016020 / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Khan, M.F. / Machuca, M.A. / Rahman, M.M. / Roujeinikova, A. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Biomolecules / Year: 2020 Title: Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by theCampylobacter jejuniChemoreceptor Tlp3. Authors: Khan, M.F. / Machuca, M.A. / Rahman, M.M. / Koc, C. / Norton, R.S. / Smith, B.J. / Roujeinikova, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6w3t.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6w3t.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/6w3t ftp://data.pdbj.org/pub/pdb/validation_reports/w3/6w3t | HTTPS FTP |
---|
-Related structure data
Related structure data | 6w3oC 6w3pC 6w3rC 6w3sC 6w3vC 6w3xC 6w3yC 4xmrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28700.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: D8X59_02240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3X8N4T9, UniProt: Q0P864*PLUS #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium citrate and ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.23 Å / Num. obs: 31594 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.45 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Rrim(I) all: 0.313 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xmr Resolution: 2.1→39.969 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.65 Å2 / Biso mean: 25.2279 Å2 / Biso min: 4.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→39.969 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|