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- PDB-5iof: Structure of the transmembrane domain of the transporter SLC26Dg -

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Basic information

Entry
Database: PDB / ID: 5iof
TitleStructure of the transmembrane domain of the transporter SLC26Dg
ComponentsSulphate transporter
KeywordsTRANSPORT PROTEIN / SLC26 family / fumarate transporter / secondary active transport
Function / homology: / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / membrane / Sulphate transporter
Function and homology information
Biological speciesDeinococcus geothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsDutzler, R. / Geertsma, E.R.G. / Shaik, F.R.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2015
Title: Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family.
Authors: Geertsma, E.R. / Chang, Y.N. / Shaik, F.R. / Neldner, Y. / Pardon, E. / Steyaert, J. / Dutzler, R.
History
DepositionMar 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
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: Sulphate transporter
B: Sulphate transporter
C: Sulphate transporter
D: Sulphate transporter


Theoretical massNumber of molelcules
Total (without water)170,2904
Polymers170,2904
Non-polymers00
Water00
1
A: Sulphate transporter


Theoretical massNumber of molelcules
Total (without water)42,5731
Polymers42,5731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulphate transporter


Theoretical massNumber of molelcules
Total (without water)42,5731
Polymers42,5731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sulphate transporter


Theoretical massNumber of molelcules
Total (without water)42,5731
Polymers42,5731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sulphate transporter


Theoretical massNumber of molelcules
Total (without water)42,5731
Polymers42,5731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.590, 82.490, 166.370
Angle α, β, γ (deg.)96.33, 92.94, 119.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sulphate transporter


Mass: 42572.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis (strain DSM 11300) (bacteria)
Strain: DSM 11300 / Gene: Dgeo_2773 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1J2S8

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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: 5.59 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 50 mM Mg-acetate, 50 mM glycine, pH 9.3, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 26246 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 4.2→4.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DA0

5da0


Resolution: 4.2→19.964 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 41.09
RfactorNum. reflection% reflection
Rfree0.312 1312 5.07 %
Rwork0.2914 --
obs0.2925 25879 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.2→19.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11096 0 0 0 11096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511312
X-RAY DIFFRACTIONf_angle_d1.09515428
X-RAY DIFFRACTIONf_dihedral_angle_d15.3143900
X-RAY DIFFRACTIONf_chiral_restr0.0421960
X-RAY DIFFRACTIONf_plane_restr0.0041888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.36650.38631520.38322734X-RAY DIFFRACTION96
4.3665-4.5630.36381410.33442733X-RAY DIFFRACTION97
4.563-4.80040.3081480.29662701X-RAY DIFFRACTION96
4.8004-5.09650.29091470.27862744X-RAY DIFFRACTION97
5.0965-5.48240.36091450.29572750X-RAY DIFFRACTION97
5.4824-6.02040.34711480.30752684X-RAY DIFFRACTION97
6.0204-6.86040.29231390.30982783X-RAY DIFFRACTION98
6.8604-8.52970.29711440.26442728X-RAY DIFFRACTION98
8.5297-19.96440.29951480.28162710X-RAY DIFFRACTION96
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.94320.9101-0.74850.77092.396212.0178-0.235-0.20180.08110.02180.094-0.05680.9072-0.26781.61370.0458-0.02611.9860.00572.0476-35.318947.8804-64
23.0526-0.33733.38991.1541.230612.8493-0.3071-0.127-0.0681-0.0785-0.3224-0.4074-0.8185-1.0521.9565-0.0170.02791.55090.00762.041-66.769221.5287-185.1326
30.9365-0.09712.61491.95234.852810.27360.0952-0.14120.0129-0.0546-0.10990.0934-0.9391-0.26021.90820.2455-0.01191.81930.03951.9779-55.523734.4183-147.0953
43.14030.4856-0.86261.08831.79783.52270.30620.2823-0.2257-0.0098-0.06570.07780.77110.81682.0586-0.04390.08152.02870.06212.0573-24.813635.3156-102.2658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 14 through 391)
2X-RAY DIFFRACTION2(chain 'B' and resid 14 through 391)
3X-RAY DIFFRACTION3(chain 'C' and resid 14 through 391)
4X-RAY DIFFRACTION4(chain 'D' and resid 14 through 391)

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