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Yorodumi- PDB-6s33: Ligand binding domain of the P. putida receptor PcaY_PP in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s33 | |||||||||
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Title | Ligand binding domain of the P. putida receptor PcaY_PP in complex with Protocatechuate | |||||||||
Components | Aromatic acid chemoreceptor | |||||||||
Keywords | SIGNALING PROTEIN / Ligand binding domain / Pseudomonas putida / chemotactic transducer / C6-ring carboxylic acids | |||||||||
Function / homology | Function and homology information chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | |||||||||
Authors | Gavira, J.A. / Mantilla, M.A. / Fernandez, M. / Krell, T. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Febs J. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s33.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s33.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 6s33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s33 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s33 | HTTPS FTP |
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-Related structure data
Related structure data | 6s18SC 6s1aC 6s37C 6s38C 6s3bC 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: 59541.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Ligand Binding domain Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pcaY, PP_2643 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q88JK6 #2: Chemical | ChemComp-ACT / | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→40.54 Å / Num. obs: 40599 / % possible obs: 97.06 % / Redundancy: 4.1 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Net I/σ(I): 11.29 |
Reflection shell | Resolution: 1.56→1.616 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 3956 / CC1/2: 0.507 / Rpim(I) all: 0.56 / Rrim(I) all: 1.15 / % possible all: 96.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S18 Resolution: 1.56→40.54 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→40.54 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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