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- PDB-9g11: sugar/H+ symporter STP6 in inward occluded conformation with gluc... -

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Basic information

Entry
Database: PDB / ID: 9g11
Titlesugar/H+ symporter STP6 in inward occluded conformation with glucose bound
ComponentsSugar transport protein 6
KeywordsMEMBRANE PROTEIN / Sugar transporter / STP / MFS
Function / homology
Function and homology information


monosaccharide transmembrane transporter activity / carbohydrate transmembrane transport / symporter activity / membrane
Similarity search - Function
Sugar transport protein STP/MST-like, plant / Sugar transport protein STP/Polyol transporter PLT, plant / Sugar/inositol transporter / Sugar transport proteins signature 2. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / CHOLESTEROL HEMISUCCINATE / Sugar transport protein 6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAndersen, C.G. / Bavnhoj, L. / Pedersen, B.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)637372European Union
CitationJournal: To Be Published
Title: Comparative biochemical analysis of the plant sugar transporters STP6 and STP10
Authors: Andersen, C.G. / Bavnhoj, L. / Driller, J.H. / Brag, S. / Pedersen, B.P.
History
DepositionJul 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar transport protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5925
Polymers55,9521
Non-polymers1,6404
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint3 kcal/mol
Surface area19800 Å2
Unit cell
Length a, b, c (Å)122.221, 122.221, 139.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein Sugar transport protein 6 / Hexose transporter 6


Mass: 55951.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: STP6, At3g05960, F2O10.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9SFG0
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4
Has ligand of interestY

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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: 5.36 Å3/Da / Density % sol: 77.05 % / Description: Rods
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG smear (PEG2000, PEG3000, PEG3500, PEG4000, PEG5000), 0.1M Hepes pH 8.0, 0.4M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 3.2→84.23 Å / Num. obs: 19456 / % possible obs: 96.5 % / Redundancy: 4.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.123 / Rrim(I) all: 0.258 / Χ2: 0.99 / Net I/σ(I): 7.3 / Num. measured all: 80631
Reflection shellResolution: 3.2→3.42 Å / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.168 / Num. measured all: 15369 / Num. unique obs: 3591 / CC1/2: 0.347 / Rpim(I) all: 0.627 / Rrim(I) all: 1.33 / Χ2: 1 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→84.23 Å / Cross valid method: FREE R-VALUE / σ(F): 232.13 / Phase error: 25.5348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 930 4.78 %
Rwork0.2265 18522 -
obs0.2303 19452 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.06 Å2
Refinement stepCycle: LAST / Resolution: 3.2→84.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 117 0 3825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473931
X-RAY DIFFRACTIONf_angle_d0.85835354
X-RAY DIFFRACTIONf_chiral_restr0.0547623
X-RAY DIFFRACTIONf_plane_restr0.0039654
X-RAY DIFFRACTIONf_dihedral_angle_d19.1984607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.34061200.27412693X-RAY DIFFRACTION95
3.37-3.580.3331930.26312458X-RAY DIFFRACTION86
3.58-3.860.30061260.24512707X-RAY DIFFRACTION94
3.86-4.240.25821500.21792484X-RAY DIFFRACTION87
4.24-4.860.22551280.19742714X-RAY DIFFRACTION94
4.86-6.120.25581750.21332688X-RAY DIFFRACTION92
6.12-84.230.20451300.23692786X-RAY DIFFRACTION92
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)
11.747727012070.5650007085840.5480568591522.323864412480.5782986242611.34350826786-0.147095041010.2626317282730.02790914915560.1937202839070.150967934056-0.220004468415-0.2406808323240.162662857011-0.05515396348540.57270861143-0.0463079269833-0.03789313186310.618006368955-0.01069429182030.46162783506663.8437490011-27.9458114196-1.37519477956
20.6901937779580.1957481853660.4538315043870.8987024337370.5695422248982.24557512735-0.0507086447963-0.132539692127-0.1128156185810.08195873973270.0534646795910.1955533591510.284953876229-0.270843121282-0.06916399198040.498995368516-0.0308162828929-0.03203461894690.4591967937220.06123487003290.39371293300949.7346177599-34.51462351476.97769074274
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 76 )17 - 761 - 60
22chain 'A' and (resid 77 through 493 )77 - 49261 - 476

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