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- PDB-5euw: Rat prestin STAS domain in complex with nitrate -

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Basic information

Entry
Database: PDB / ID: 5euw
TitleRat prestin STAS domain in complex with nitrate
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
NITRATE ION / DI(HYDROXYETHYL)ETHER / Prestin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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

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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)16,4218
Polymers15,7671
Non-polymers6557
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint14 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.223, 62.223, 66.873
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, 101 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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-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.: 94 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
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, 100 mM NaNO3, 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: 1.2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.81→41.96 Å / Num. all: 89717 / Num. obs: 14062 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Rsym value: 0.082 / Net I/σ(I): 15
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 1.7 / % possible all: 97.2

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Processing

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

3llo


Resolution: 1.81→41.959 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 770 5.49 %
Rwork0.1641 13263 -
obs0.1655 14033 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.62 Å2 / Biso mean: 39.0268 Å2 / Biso min: 15.96 Å2
Refinement stepCycle: final / Resolution: 1.81→41.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 99 94 1207
Biso mean--67.75 42.76 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081071
X-RAY DIFFRACTIONf_angle_d1.0571441
X-RAY DIFFRACTIONf_chiral_restr0.043164
X-RAY DIFFRACTIONf_plane_restr0.004183
X-RAY DIFFRACTIONf_dihedral_angle_d14.997387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8099-1.92320.30761190.24162161228099
1.9232-2.07170.23481420.184921772319100
2.0717-2.28020.21511150.155221902305100
2.2802-2.61010.17311490.149121792328100
2.6101-3.28830.18211310.167122202351100
3.2883-41.97060.17431140.156823362450100
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)
14.7111-0.5193-0.71165.0192-0.03157.23180.1019-0.1343-0.24540.0724-0.0213-0.47630.0990.649-0.0250.1666-0.016-0.07250.1923-0.04650.294-14.66642.8994-1.9031
25.2352-0.9956-0.32263.83122.98757.9413-0.2137-1.053-0.15861.62150.038-0.63210.51440.12450.17110.73540.0035-0.10260.36090.0770.3718-26.6404-0.717411.7168
37.77443.107-1.61025.6987-0.10463.2178-0.0865-0.24810.06230.49620.0339-0.0270.1543-0.07750.03460.24290.0278-0.03920.12180.02210.1338-29.11815.12324.7956
44.54981.88081.11515.3172.18484.38-0.0599-0.23670.33220.6523-0.09130.3689-0.1229-0.26990.09960.3190.01010.0280.144-0.01050.2035-33.344611.60386.4281
58.69511.5457-1.34254.0475-0.86663.56210.3042-0.28320.2813-0.01520.00230.0264-0.5433-0.0238-0.19980.2577-0.0243-0.00790.14560.00310.1838-25.41916.4617-2.2196
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 658 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 659 through 697 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 698 through 718 )A0

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