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Yorodumi- PDB-6w3y: Crystal structure of ligand-binding domain of Campylobacter jejun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w3y | ||||||
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Title | Crystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with L-alanine | ||||||
Components | Methyl-accepting chemotaxis protein | ||||||
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: 1.32 Å | ||||||
Authors | Khan, M.F. / Machuca, M.A. / Rahman, M.M. / Roujeinikova, A. | ||||||
Funding support | Australia, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w3y.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w3y.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/6w3y ftp://data.pdbj.org/pub/pdb/validation_reports/w3/6w3y | HTTPS FTP |
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-Related structure data
Related structure data | 6w3oC 6w3pC 6w3rC 6w3sC 6w3tC 6w3vC 6w3xC 4xmrS 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 807 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.5 Å3/Da / Density % sol: 50.76 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→46.12 Å / Num. obs: 128662 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.32→1.34 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xmr Resolution: 1.32→46.12 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.402 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.87 Å2 / Biso mean: 20.369 Å2 / Biso min: 8.21 Å2
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Refinement step | Cycle: final / Resolution: 1.32→46.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.353 Å / Rfactor Rfree error: 0
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