+Open data
-Basic information
Entry | Database: PDB / ID: 5eux | |||||||||
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Title | Rat prestin STAS domain in complex with thiocyanate | |||||||||
Components | Prestin,Prestin | |||||||||
Keywords | TRANSPORT PROTEIN / Anion-binding site / protein-anion complex | |||||||||
Function / homology | Function and homology information oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transport / response to auditory stimulus ...oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / monoatomic anion transmembrane transport / response to auditory stimulus / response to potassium ion / response to salt / chloride:bicarbonate antiporter activity / response to thyroid hormone / bicarbonate transport / bicarbonate transmembrane transporter activity / positive regulation of cell motility / chloride transport / chloride transmembrane transporter activity / spectrin binding / cochlea development / cytoskeletal motor activity / positive regulation of cell size / lateral plasma membrane / chloride transmembrane transport / monoatomic ion transmembrane transport / regulation of membrane potential / response to ischemia / sensory perception of sound / regulation of cell shape / basolateral plasma membrane / response to xenobiotic stimulus / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.038 Å | |||||||||
Authors | Lolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R. | |||||||||
Funding support | 2items
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Citation | Journal: Biochem.J. / Year: 2016 Title: The STAS domain of mammalian SLC26A5 prestin harbours an anion-binding site. Authors: Lolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R. #1: Journal: J. Mol. Biol. / Year: 2010 Title: Structure of the cytosolic portion of the motor protein prestin and functional role of the STAS domain in SLC26/SulP anion transporters. Authors: Pasqualetto, E. / Aiello, R. / Gesiot, L. / Bonetto, G. / Bellanda, M. / Battistutta, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eux.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eux.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5eux ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eux | HTTPS FTP |
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-Related structure data
Related structure data | 5eusC 5euuC 5euwC 5euzC 5ezbC 3lloS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15766.707 Da / Num. of mol.: 1 / Fragment: STAS domain,STAS domain Mutation: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637 Source method: isolated from a genetically manipulated source Details: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637 Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc26a5, Pres / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9EPH0 |
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-Non-polymers , 5 types, 48 molecules
#2: Chemical | ChemComp-SCN / | ||
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#3: Chemical | ChemComp-PEG / | ||
#4: Chemical | ChemComp-PG4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Mes pH 6.5, 1.8 M Ammonium Sulphate, 250 mM NaSCN, 5% (w/v) PEG400, 0.1% (w/v) octyl-beta-D-glucopyranoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 2 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 2.038→41.99 Å / Num. all: 168644 / Num. obs: 9671 / % possible obs: 97.4 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.085 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.04→2.09 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 2.1 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LLO Resolution: 2.038→41.988 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.88 Å2 / Biso mean: 53.8769 Å2 / Biso min: 24.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.038→41.988 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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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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