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Yorodumi- PDB-5g4y: Structural basis for carboxylic acid recognition by a Cache chemo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g4y | ||||||
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Title | Structural basis for carboxylic acid recognition by a Cache chemosensory domain. | ||||||
Components | Methyl-accepting chemotaxis sensory transducer with Cache sensor | ||||||
Keywords | SIGNALING PROTEIN / CHEMOTAXIS / CHEMORECEPTORS / LIGAND BINDING DOMAINS / METHYL- ACCEPTING CHEMOTAXIS PROTEINS | ||||||
Function / homology | Function and homology information chemotaxis / transmembrane signaling receptor activity / membrane => GO:0016020 / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Brewster, J. / McKellar, J.L.O. / Newman, J. / Peat, T.S. / Gerth, M.L. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Authors: Brewster, J.L. / McKellar, J.L. / Finn, T.J. / Newman, J. / Peat, T.S. / Gerth, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4y.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4y.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 5g4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4y ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4y | HTTPS FTP |
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-Related structure data
Related structure data | 5g4zC 4k08S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 20182.893 Da / Num. of mol.: 1 / Fragment: C2-CHEMORECEPTOR SENSOR DOMAIN, RESIDUES 34-181 Source method: isolated from a genetically manipulated source Details: MISSING N-TERMINAL DOMAIN / Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: BCD74_10458 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S3VA52 |
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL AND C-TERMINAL DOMAINS REMOVED. JUST THE CACHE C2 CHEMORECEP |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROTEIN AT 8.5 MG/ML IN 50 MM BIS-TRIS CHLORIDE, PH 6.5, 50 MM SODIUM CHLORIDE IN EQUAL VOLUME WITH 27% PEG 4000 AND 100 MM PROLINE AT 20 C IN SITTING DROPS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 11, 2015 |
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→48.8 Å / Num. obs: 16085 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.9 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K08 Resolution: 2→64.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.212 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY LIGAND IS ASSUMED TO BE PROPIONATE AS THAT FITS THE DENSITY WELL, BUT NO PROPIONATE WAS ADDED TO THE PROTEIN OR CRYSTALS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2→64.33 Å
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Refine LS restraints |
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