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- PDB-5ezb: Chicken prestin STAS domain -

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Basic information

Entry
Database: PDB / ID: 5ezb
TitleChicken prestin STAS domain
ComponentsChicken prestin STAS domain,Chicken prestin STAS domain
KeywordsTRANSPORT PROTEIN / Eukaryotic SLC26 STAS fold
Function / homology
Function and homology information


sulfate:chloride antiporter activity / oxalate:chloride antiporter activity / sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / sulfate transmembrane transport / bicarbonate transmembrane transporter activity / chloride transmembrane transporter activity / chloride transmembrane transport / metal ion 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
OXALATE ION / Prestin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 26, 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 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chicken prestin STAS domain,Chicken prestin STAS domain
B: Chicken prestin STAS domain,Chicken prestin STAS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2987
Polymers31,9642
Non-polymers3345
Water97354
1
A: Chicken prestin STAS domain,Chicken prestin STAS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1634
Polymers15,9821
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chicken prestin STAS domain,Chicken prestin STAS domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1353
Polymers15,9821
Non-polymers1532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.551, 56.919, 101.140
Angle α, β, γ (deg.)90.000, 96.190, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 513 - 730 / Label seq-ID: 3 - 140

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chicken prestin STAS domain,Chicken prestin STAS domain


Mass: 15982.049 Da / Num. of mol.: 2 / Fragment: STAS domain,STAS domain
Mutation: Residues 570-651 (variable loop) are deleted, GlySer are inserted between position 569 and 652,Residues 570-651 (variable loop) are deleted, GlySer are inserted between position 569 and 652
Source method: isolated from a genetically manipulated source
Details: Residues 570-651 (variable loop) are deleted, GlySer are inserted between position 569 and 652
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SLC26A5, slc26A5 / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0FKN5

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Non-polymers , 5 types, 59 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 1.5 M Ammonium Sulphate, 12% (v/v) glycerol, 0.3 M Ammonium oxalate

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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 23, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→46.59 Å / Num. obs: 19970 / % possible obs: 96.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.8 / % possible all: 96.9

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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: 2.3→46.585 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 1016 5.12 %
Rwork0.2198 18834 -
obs0.2217 19850 95.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.58 Å2 / Biso mean: 55.1761 Å2 / Biso min: 28.72 Å2
Refinement stepCycle: final / Resolution: 2.3→46.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 23 54 2227
Biso mean--61.31 46.15 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152200
X-RAY DIFFRACTIONf_angle_d1.2952983
X-RAY DIFFRACTIONf_chiral_restr0.069346
X-RAY DIFFRACTIONf_plane_restr0.007384
X-RAY DIFFRACTIONf_dihedral_angle_d14.093789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1566X-RAY DIFFRACTION7.048TORSIONAL
12B1566X-RAY DIFFRACTION7.048TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.41890.30341610.27392732X-RAY DIFFRACTION97
2.4189-2.57050.30281320.25282751X-RAY DIFFRACTION99
2.5705-2.76890.31191190.26992108X-RAY DIFFRACTION76
2.7689-3.04750.27241540.25642800X-RAY DIFFRACTION100
3.0475-3.48840.29771380.26012799X-RAY DIFFRACTION99
3.4884-4.39450.27991400.21792790X-RAY DIFFRACTION98
4.3945-46.59460.19211720.15942854X-RAY DIFFRACTION100

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