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- PDB-5eux: Rat prestin STAS domain in complex with thiocyanate -

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Basic information

Entry
Database: PDB / ID: 5eux
TitleRat prestin STAS domain in complex with thiocyanate
ComponentsPrestin,Prestin
KeywordsTRANSPORT 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 / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / response to thyroid hormone / negative regulation of monoatomic ion transmembrane transport ...oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / secondary active sulfate transmembrane transporter activity / response to thyroid hormone / negative regulation of monoatomic ion transmembrane transport / response to potassium ion / monoatomic anion transmembrane transport / response to auditory stimulus / chloride:bicarbonate antiporter activity / response to salt / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transport / chloride transmembrane transporter activity / positive regulation of cell motility / spectrin binding / cytoskeletal motor activity / cochlea development / lateral plasma membrane / positive regulation of cell size / chloride transmembrane transport / response to ischemia / regulation of membrane potential / sensory perception of sound / regulation of cell shape / monoatomic ion transmembrane transport / basolateral plasma membrane / response to xenobiotic stimulus / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
STAS domain / Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / Transcription Regulator spoIIAA / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain ...STAS domain / Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / Transcription Regulator spoIIAA / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Prestin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.038 Å
AuthorsLolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R.
Funding support2items
OrganizationGrant numberCountry
European Community's Seventh Framework Programme (FP7/2007-2013) under BioStruct-Xgrant agreement Number 283570)
Fondazione Cassa di Risparmio di Padova e RovigoProgetto di Eccellenza
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
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prestin,Prestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3117
Polymers15,7671
Non-polymers5456
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint8 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.365, 62.365, 66.755
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prestin,Prestin / Solute carrier family 26 member 5


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 / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.04→2.09 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 2.1 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLO

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
RfactorNum. reflection% reflection
Rfree0.1977 951 5.28 %
Rwork0.163 17069 -
obs0.1648 9652 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.88 Å2 / Biso mean: 53.8769 Å2 / Biso min: 24.67 Å2
Refinement stepCycle: final / Resolution: 2.038→41.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 81 42 1137
Biso mean--78.18 47.26 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161064
X-RAY DIFFRACTIONf_angle_d1.2591433
X-RAY DIFFRACTIONf_chiral_restr0.055164
X-RAY DIFFRACTIONf_plane_restr0.006181
X-RAY DIFFRACTIONf_dihedral_angle_d14.997383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0376-2.14510.28961540.22932240239489
2.1451-2.27950.287890.20122432252195
2.2795-2.45540.2131300.19572412254296
2.4554-2.70250.22971450.19312479262498
2.7025-3.09340.22281700.1762459262999
3.0934-3.8970.2031260.154825262652100
3.897-41.99690.15311370.138825212658100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61770.50440.71470.92150.19370.7913-0.0037-0.0465-0.52090.05880.1761-0.18180.46950.14690.00050.3910.0055-0.0340.41480.04650.4988-5.74512.8425-14.8143
20.234-0.13130.270.8179-0.38930.1190.2829-0.3838-0.05970.4268-0.22290.02550.2959-0.2244-0.00050.3242-0.1009-0.01520.5160.02310.4149-9.353520.8578-4.4246
30.0119-0.02650.0130.01270.01460.12960.57360.12430.69611.06880.2211-0.7123-0.0797-0.096-0.00150.5930.0350.02531.23390.1511.2173-8.563119.51586.6089
40.7271-0.1576-0.21591.08390.1870.35510.3218-0.4323-0.07470.3373-0.2669-0.03650.0932-0.106-0.00010.2665-0.0714-0.01580.4862-0.00310.2817-9.203728.7308-4.2067
50.68430.52830.2491.42530.3109-0.07160.1959-0.26590.16610.2404-0.17980.0438-0.0793-0.07500.2825-0.0251-0.02020.4667-0.02860.3207-7.642934.1444-6.2538
60.25350.1465-0.20661.0416-0.69880.7561-0.1989-1.04420.5165-0.60270.1556-0.4997-0.37730.4678-0.07450.3922-0.0488-0.06410.4924-0.1390.3897-3.035140.4049-6.8132
70.31960.2018-0.48670.4806-0.2210.1160.0039-0.0054-0.0671-0.03670.28060.0688-0.09980.17850.00120.2301-0.0293-0.01480.4287-0.02840.29622.168528.6093-14.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 506 through 530 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 531 through 550 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 551 through 553 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 638 through 666 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 667 through 692 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 693 through 701 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 702 through 718 )A0

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