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- PDB-5da0: Structure of the the SLC26 transporter SLC26Dg in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 5da0
TitleStructure of the the SLC26 transporter SLC26Dg in complex with a nanobody
Components
  • Nanobody
  • Sulphate transporter
KeywordsTRANSPORT PROTEIN / Membrane transport protein / nanobody complex
Function / homology
Function and homology information


SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sulphate transporter
Similarity search - Component
Biological speciesDeinococcus geothermalis (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsDutzler, R. / Geertsma, E.R. / Chang, Y. / Shaik, F.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
SNSFNCCR Structural Biology Switzerland
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
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulphate transporter
B: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3314
Polymers67,3662
Non-polymers9652
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-15 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.650, 117.280, 84.360
Angle α, β, γ (deg.)90.00, 100.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-219-

LEU

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Components

#1: Antibody Sulphate transporter


Mass: 54148.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis (strain DSM 11300) (bacteria)
Gene: Dgeo_2773 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1J2S8
#2: Antibody Nanobody


Mass: 13217.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.61 Å3/Da / Density % sol: 73.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1M Ammoniumformate, 50 mM Na Acetate pH 4.5, 48% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 20209 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.7
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
DMphasing
RefinementResolution: 3.2→19.946 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.308 973 4.85 %
Rwork0.2584 --
obs0.2609 20070 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 66 0 4412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034502
X-RAY DIFFRACTIONf_angle_d0.7446113
X-RAY DIFFRACTIONf_dihedral_angle_d12.8611557
X-RAY DIFFRACTIONf_chiral_restr0.026746
X-RAY DIFFRACTIONf_plane_restr0.004754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.36810.47131640.37492681X-RAY DIFFRACTION99
3.3681-3.5780.36081200.33052718X-RAY DIFFRACTION99
3.578-3.85250.31551480.3042697X-RAY DIFFRACTION99
3.8525-4.23680.29681090.27012768X-RAY DIFFRACTION100
4.2368-4.84220.30221440.25022723X-RAY DIFFRACTION100
4.8422-6.0720.32981490.26992742X-RAY DIFFRACTION100
6.072-19.94610.2721390.21782768X-RAY DIFFRACTION99
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)
10.0326-0.44670.03840.6677-0.83520.7999-0.0412-0.18260.04220.15940.1012-0.07970.02180.479701.0398-0.0331-0.01720.9699-0.00160.996461.583120.919965.5601
2-0.19850.48871.11640.9901-0.86470.6976-0.14510.4088-0.0839-0.07840.11090.0812-0.48610.2352-01.2029-0.24750.09560.9703-0.0051.099655.168837.817663.9227
30.60460.2529-0.14020.59410.27443.4776-0.12620.3063-0.08070.02440.0251-0.0666-0.0860.147701.0132-0.04650.02081.0110.03121.034354.808724.44762.9745
40.6284-0.05220.35790.98620.36360.0823-0.33260.6194-0.3151-0.16430.23370.0970.21290.292201.1872-0.0936-0.04221.578-0.02891.257311.387518.066943.6704
50.1548-0.1296-0.17660.0732-0.2098-0.3574-0.088-0.63740.11620.61340.6873-0.6881-0.7305-1.101201.67770.16690.05981.8434-0.22652.0201-10.888428.47661.5456
60.147-0.07820.12150.15230.3404-0.02550.1285-1.76220.91690.74730.95330.6081-0.4728-0.461201.34920.2287-0.08941.7192-0.23711.63032.612328.534956.5889
70.11950.0138-0.05110.0416-0.0662-0.1276-0.7786-0.978-0.3230.2117-0.1496-0.4216-0.5254-0.5689-01.63540.00110.23332.06150.14051.8061-2.352222.137649.7368
8-0.04060.0034-0.0363-0.00290.04580.0191-0.23370.13030.3082-0.1970.05990.44350.1419-0.126802.00410.4665-0.09022.4694-0.34831.8382-6.948436.249448.4585
90.1643-0.0745-0.03010.16030.0688-0.0190.1887-0.77480.7812-0.0534-0.4165-0.00940.96930.3476-01.57280.0252-0.05551.821-0.14931.6461-5.525724.70859.6944
10-0.0160.29220.0916-0.0205-0.0223-0.1148-0.7294-0.81330.6628-0.04050.5448-0.41850.11590.224101.9477-0.0157-0.07832.767-0.27642.21114.373831.707157.3173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 391 )
4X-RAY DIFFRACTION4chain 'A' and (resid 392 through 484 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 55 )
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 71 )
8X-RAY DIFFRACTION8chain 'B' and (resid 72 through 80 )
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 100 )
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 124 )

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