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- PDB-3llo: Crystal structure of the STAS domain of motor protein prestin (an... -

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Basic information

Entry
Database: PDB / ID: 3llo
TitleCrystal structure of the STAS domain of motor protein prestin (anion transporter SLC26A5)
ComponentsPrestin
KeywordsMOTOR PROTEIN / STAS domain / Cell shape / Glycoprotein / Membrane / Transmembrane
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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.57 Å
AuthorsPasqualetto, E. / Aiello, R. / Bonetto, G. / Battistutta, R.
CitationJournal: 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
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0592
Polymers15,7671
Non-polymers2921
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.590, 61.590, 67.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 15766.707 Da / Num. of mol.: 1 / Fragment: UNP residues 505-563, 637-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc26a5, Pres / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EPH0
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Description: The Structure Factor File contains Friedel Pairs
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1.8 M Ammonium sulfate, 4.5% (v/v) PEG 400, 0.1% (w/v) octyl-beta-D-glucopyranoside, 0.09 M MES, pH 6.5, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 8, 2009
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionRedundancy: 32.7 % / Av σ(I) over netI: 6.5 / Number: 660833 / Rsym value: 0.066 / D res high: 1.6 Å / D res low: 53.64 Å / Num. obs: 20184 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.0641.9399.710.0410.04129.1
3.585.0610010.0460.04632.2
2.923.5810010.0570.05732.6
2.532.9210010.0570.05733
2.262.5310010.0590.05933.1
2.072.2610010.0760.07633.1
1.912.0710010.1170.11733.1
1.791.9110010.1940.19433.1
1.691.7910010.3240.32433.1
1.61.6910010.5130.51332.4
ReflectionResolution: 1.57→28.408 Å / Num. all: 20860 / Num. obs: 20860 / % possible obs: 99.3 % / Redundancy: 11.3 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 8.5
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2931 / Rsym value: 0.496 / % possible all: 97.6

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MRRfactor: 28.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.41 Å
Translation2.5 Å28.41 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 20160
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.69-10029.60.663504
4.47-5.6928.90.895513
3.88-4.4730.20.901503
3.51-3.8830.20.891503
3.25-3.5127.10.917508
3.04-3.2528.60.914536
2.87-3.04310.906567
2.73-2.8731.20.896596
2.6-2.7332.20.899609
2.49-2.631.80.913650
2.39-2.4930.10.912677
2.31-2.3931.20.897709
2.23-2.31310.915712
2.16-2.2331.60.911756
2.1-2.1631.60.903780
2.04-2.1340.911782
1.98-2.0432.50.907805
1.93-1.9835.30.908836
1.89-1.93340.896857
1.84-1.8934.90.9869
1.8-1.8435.90.891896
1.77-1.834.80.896892
1.73-1.77350.897932
1.7-1.7335.50.885958
1.67-1.734.40.897944
1.64-1.6739.30.879984
1.6-1.6437.90.8511282

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
SHELXphasing
DM6.1phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.677 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1062 5.1 %RANDOM
Rwork0.154 ---
all0.156 20831 --
obs0.156 20831 99.143 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.27 Å2 / Biso mean: 25.149 Å2 / Biso min: 11.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.57→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 10 103 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221082
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9661476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98925.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16715172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.635152
X-RAY DIFFRACTIONr_chiral_restr0.1650.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021822
X-RAY DIFFRACTIONr_mcbond_it2.5511.5668
X-RAY DIFFRACTIONr_mcangle_it3.90221089
X-RAY DIFFRACTIONr_scbond_it5.7363414
X-RAY DIFFRACTIONr_scangle_it8.5564.5383
X-RAY DIFFRACTIONr_rigid_bond_restr2.94931082
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 92 -
Rwork0.195 1387 -
all-1479 -
obs-1479 97.05 %

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