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- PDB-5eus: Rat prestin STAS domain in complex with bromide -

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Basic information

Entry
Database: PDB / ID: 5eus
TitleRat prestin STAS domain in complex with bromide
ComponentsPrestin,Rat prestin STAS domain
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 / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus ...oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus / monoatomic anion transmembrane transport / 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 / monoatomic ion transmembrane transport / chloride 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
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
BROMIDE ION / Prestin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 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 1.2Jul 20, 2016Group: Database references
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,Rat prestin STAS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2897
Polymers15,7671
Non-polymers5226
Water1,24369
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint11 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.408, 61.408, 66.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Prestin,Rat prestin STAS domain / 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
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc26a5, Pres, slc26A5 / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9EPH0
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
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, 126 mM Potassium Bromide, 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: 0.91 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.83→41.513 Å / Num. all: 255516 / Num. obs: 13128 / % possible obs: 99.9 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.082 / Net I/σ(I): 25
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 17.9 % / Rmerge(I) obs: 1.998 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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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: 1.833→41.513 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1966 1308 5.33 %
Rwork0.1525 23247 -
obs0.1548 24555 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.87 Å2 / Biso mean: 46.2562 Å2 / Biso min: 20.71 Å2
Refinement stepCycle: final / Resolution: 1.833→41.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 72 69 1155
Biso mean--67.66 46.54 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111059
X-RAY DIFFRACTIONf_angle_d1.2191430
X-RAY DIFFRACTIONf_chiral_restr0.055164
X-RAY DIFFRACTIONf_plane_restr0.006182
X-RAY DIFFRACTIONf_dihedral_angle_d15.395380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.833-1.90640.26611700.26042526269698
1.9064-1.99320.29141440.222325712715100
1.9932-2.09830.23881680.171925642732100
2.0983-2.22970.17221360.1525972733100
2.2297-2.40190.21751360.145326072743100
2.4019-2.64350.19281260.148225852711100
2.6435-3.0260.22311220.155526362758100
3.026-3.8120.18831840.147725422726100
3.812-41.52330.17041220.139526192741100
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)
10.5159-0.2064-0.22430.3821-0.20970.37180.1924-0.10310.11870.00190.03240.2154-0.053-0.2770.00030.3054-0.02350.04460.28730.03870.345914.0381-2.8275-1.8433
20.1035-0.0558-0.07660.02840.02930.0910.0212-0.54140.30750.3864-0.25360.3794-0.47750.3021-0.00240.5053-0.06830.07740.359-0.09220.403726.31240.90611.4293
31.2489-0.15050.28931.4547-0.36670.69720.0361-0.1099-0.06040.18670.0236-0.06120.12120.091400.3389-0.02810.01110.24430.02090.245329.6206-11.16133.6414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 505 through 539 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 540 through 552 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 638 through 718)A0

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