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Yorodumi- PDB-5g4z: Structural basis for carboxylic acid recognition by a Cache chemo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g4z | ||||||
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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 / PSEUDOMONAS SYRINGAE PV. ACTINIDIAE | ||||||
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: 1.98 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 | 5g4z.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4z.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4z ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4z | HTTPS FTP |
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-Related structure data
Related structure data | 5g4ySC 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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-Components
#1: Protein | Mass: 20182.893 Da / Num. of mol.: 1 / Fragment: C2-CHEMORECEPTOR SENSOR DOMAIN RESIDUES 34-191 Source method: isolated from a genetically manipulated source Details: N-TERMINAL DOMAIN (33 RESIDUES) AND C- TERMINAL DOMAIN (353 RESIDUES) REMOVED. JUST THE C2 CACHE SENSOR DOMAIN IS CRYSTALLIZED. 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: Chemical | ChemComp-PGE / |
#4: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL HIS-TAG IN PLACE OF THE NATIVE N-TERMINAL 33 AMINO ACIDS AND THE C-TERMINAL DOMAIN (OF ...N-TERMINAL HIS-TAG IN PLACE OF THE NATIVE N-TERMINAL 33 AMINO ACIDS AND THE C-TERMINAL DOMAIN (OF 353 RESIDUES) IS REMOVED LEAVING JUST THE C2 CACHE CHEMOSENSO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.1 % / 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 BISTRIS CHLORIDE, PH 6.5, 50 MM SODIUM CHLORIDE IN EQUAL VOLUME WITH 27% PEG 4000 AND 3% SUCROSE AT 20 C IN SITTING DROP PLATES. CRYSTALS WERE LATER SOAKED IN ...Details: PROTEIN AT 8.5 MG/ML IN 50 MM BISTRIS CHLORIDE, PH 6.5, 50 MM SODIUM CHLORIDE IN EQUAL VOLUME WITH 27% PEG 4000 AND 3% SUCROSE AT 20 C IN SITTING DROP PLATES. CRYSTALS WERE LATER SOAKED IN RESERVOIR SOLUTION WITH 40 MM NEUTRALIZED PROPIONATE. |
-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: Feb 19, 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: 1.98→48.5 Å / Num. obs: 16058 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G4Y Resolution: 1.98→63.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.109 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→63.59 Å
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