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- PDB-5euz: Rat prestin STAS domain in complex with iodide -

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Basic information

Entry
Database: PDB / ID: 5euz
TitleRat prestin STAS domain in complex with iodide
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 / secondary active sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / response to auditory stimulus / response to potassium ion ...oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / response to auditory stimulus / response to potassium ion / monoatomic anion transmembrane transport / chloride:bicarbonate antiporter activity / response to thyroid hormone / response to salt / 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 / regulation of membrane potential / response to ischemia / 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 / SLC26A/SulP transporter domain / Sulfate permease family / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain ...STAS domain / Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Prestin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsLolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R.
Funding support Italy, 2items
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 Italy
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 1.2Jan 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)16,99413
Polymers15,8141
Non-polymers1,18012
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint14 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.911, 61.911, 66.490
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: 15813.604 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. Met651SeMet,Residues 564-636 (variable loop) are deleted, GlySer are inserted between ...Mutation: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637. Met651SeMet,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637. Met651SeMet
Source method: isolated from a genetically manipulated source
Details: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637. Met651SeMet
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, 43 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.28 %
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, 5% (w/v) PEG400, 0.1% (w/v) octyl-beta-D-glucopyranoside. Crystals were soaked with precipitant solution supplemented with 0.5 M Potassium Iodide

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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: Jul 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.4→41.74 Å / Num. all: 89114 / Num. obs: 6054 / % possible obs: 99.8 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.161 / Rsym value: 0.172 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.733 / Mean I/σ(I) obs: 1.7 / % possible all: 98.1

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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: 2.403→41.737 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 652 5.89 %
Rwork0.1883 10414 -
obs0.1903 11066 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.38 Å2 / Biso mean: 55.2479 Å2 / Biso min: 22.19 Å2
Refinement stepCycle: final / Resolution: 2.403→41.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 112 31 1166
Biso mean--64.9 40.74 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031080
X-RAY DIFFRACTIONf_angle_d0.7931451
X-RAY DIFFRACTIONf_chiral_restr0.03165
X-RAY DIFFRACTIONf_plane_restr0.003184
X-RAY DIFFRACTIONf_dihedral_angle_d16.339388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4033-2.58880.30771540.26912026218097
2.5888-2.84930.2999960.243121112207100
2.8493-3.26140.23331240.215821232247100
3.2614-4.10850.24471420.170220782220100
4.1085-41.74340.16921360.160620762212100
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)
10.2656-0.06920.01810.1670.29910.14260.2207-0.05060.0575-0.34570.1629-0.22750.20880.3021-00.3665-0.0251-0.00160.2832-0.04840.445814.381456.137763.6237
20.47160.06790.31630.4991-0.21620.5408-0.0087-0.0878-0.04710.16080.0442-0.11690.09150.181-00.34170.0048-0.03940.3382-0.0330.380914.139655.346267.5188
30.029-0.02660.00840.0166-0.05840.01280.5939-1.0687-0.3252-0.17670.08440.4658-0.2368-0.63601.0655-0.0532-0.11550.73050.10060.77066.369453.400381.6157
40.9156-0.19650.0692.33460.13271.0176-0.1065-0.00030.0020.10550.12460.069-0.0135-0.082700.2735-0.0003-0.00950.2392-0.01550.22810.856964.629370.2386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 505 through 520 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 521 through 545)A0
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 552 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 638 through 718 )A0

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