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- PDB-6s37: Ligand binding domain of the P. putida receptor PcaY_PP in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s37 | |||||||||
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Title | Ligand binding domain of the P. putida receptor PcaY_PP in complex with salicylic acid | |||||||||
![]() | Aromatic acid chemoreceptor | |||||||||
![]() | SIGNALING PROTEIN / Ligand binding domain / Pseudomonas putida / chemotactic transducer / C6-ring carboxylic acids | |||||||||
Function / homology | ![]() transmembrane signaling receptor activity / chemotaxis / signal transduction / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gavira, J.A. / Mantilla, M.A. / Fernandez, M. / Krell, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural basis for signal promiscuity in a bacterial chemoreceptor. Authors: Gavira, J.A. / Matilla, M.A. / Fernandez, M. / Krell, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144 KB | Display | ![]() |
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PDB format | ![]() | 107.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.5 KB | Display | ![]() |
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Full document | ![]() | 763.9 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6s18SC ![]() 6s1aC ![]() 6s33C ![]() 6s38C ![]() 6s3bC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59541.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Ligand binding domain Source: (gene. exp.) ![]() Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaY, PP_2643 Production host: ![]() ![]() References: UniProt: Q88JK6 #2: Chemical | ChemComp-SAL / | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 33 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 6.5 Details: 30% PEG 8K, 0.1M Na Acetate, 0.1M Na-Cacodylate pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40.44 Å / Num. obs: 13404 / % possible obs: 98.97 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.054 / Rrim(I) all: 0.127 / Net I/σ(I): 12.44 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.58 / Num. unique obs: 1321 / CC1/2: 0.627 / Rpim(I) all: 0.559 / Rrim(I) all: 1.27 / % possible all: 99.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S18 Resolution: 2.3→40.44 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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