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- PDB-9olp: Crystal structure of a raffinose-bound D59C MelB -

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Basic information

Entry
Database: PDB / ID: 9olp
TitleCrystal structure of a raffinose-bound D59C MelB
ComponentsMelibiose permease
KeywordsMEMBRANE PROTEIN / raffinose / MFS / transporter / ligand binding
Function / homology
Function and homology information


symporter activity / sodium ion transport / carbohydrate transport / transmembrane transport / plasma membrane
Similarity search - Function
Sodium:galactoside symporter / Sodium:galactoside symporter, conserved site / Sodium:galactoside symporter family signature. / Lactose permease-like / MFS/sugar transport protein / MFS transporter superfamily
Similarity search - Domain/homology
raffinose / Melibiose permease
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 101966 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGuan, L. / Hariharan, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153222 United States
Citation
Journal: Elife / Year: 2026
Title: Allosteric effects of the coupling cation in melibiose transporter MelB.
Authors: Hariharan, P. / Shi, Y. / Bakhtiiari, A. / Liang, R. / Viner, R. / Guan, L.
#1: Journal: Elife / Year: 2026
Title: Allosteric effects of the coupling cation in melibiose transporter MelB
Authors: Hariharan, P. / Shi, Y. / Amirhossein, B. / Liang, R. / Viner, R. / Guan, L.
History
DepositionMay 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melibiose permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5972
Polymers54,0921
Non-polymers5041
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, cryoEM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.103, 127.103, 104.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Melibiose permease / Melibiose carrier / Melibiose transporter / Melibiose/cation symporter / Na+ (Li+)/melibiose ...Melibiose carrier / Melibiose transporter / Melibiose/cation symporter / Na+ (Li+)/melibiose symporter / Thiomethylgalactoside permease II


Mass: 54092.496 Da / Num. of mol.: 1 / Mutation: D59C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 101966 (bacteria)
Strain: LT2 / Gene: melB, STM4299 / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / References: UniProt: P30878
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationN

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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: 4.52 Å3/Da / Density % sol: 73.33 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, 100 mM, PH 8.5, BaCl2, 50 mM, CaCl2, 50 mM, PEG400, 32.5%
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.31→47.34 Å / Num. obs: 14954 / % possible obs: 99.9 % / Redundancy: 19.4 % / Biso Wilson estimate: 95.88 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.279 / Rpim(I) all: 0.092 / Rrim(I) all: 0.293 / Net I/σ(I): 10.3
Reflection shellResolution: 3.31→3.58 Å / Redundancy: 19.4 % / Rmerge(I) obs: 2.845 / Num. unique obs: 3035 / CC1/2: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASER1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→19.89 Å / SU ML: 0.9457 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 48.3436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3288 1327 10.02 %
Rwork0.3158 11910 -
obs0.3171 13237 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.7 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 34 0 3581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253675
X-RAY DIFFRACTIONf_angle_d0.56475009
X-RAY DIFFRACTIONf_chiral_restr0.0361597
X-RAY DIFFRACTIONf_plane_restr0.0038600
X-RAY DIFFRACTIONf_dihedral_angle_d11.45441322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.540.49991400.51951284X-RAY DIFFRACTION93.68
3.54-3.690.59141430.56641217X-RAY DIFFRACTION92.64
3.7-3.890.511350.541233X-RAY DIFFRACTION90.3
3.89-4.130.47361390.4421250X-RAY DIFFRACTION91.93
4.13-4.450.3191480.29051367X-RAY DIFFRACTION99.93
4.45-4.890.26481530.26781364X-RAY DIFFRACTION99.93
4.89-5.580.29641550.27441370X-RAY DIFFRACTION100
5.58-6.980.37921530.31531395X-RAY DIFFRACTION100
6.98-19.890.22021610.21251430X-RAY DIFFRACTION99.25
Refinement TLS params.Method: refined / Origin x: -25.0918498735 Å / Origin y: 50.5964382782 Å / Origin z: -6.05144656764 Å
111213212223313233
T0.51782375906 Å2-0.142214941414 Å20.0524519828723 Å2-1.18169484807 Å20.0279968633209 Å2--1.26728385046 Å2
L1.7640515552 °20.422117423135 °20.564259081286 °2-2.18039370705 °20.130732973943 °2--2.95743029478 °2
S0.478159761157 Å °0.470606368133 Å °-0.0639981722737 Å °0.151406304233 Å °-0.299164239587 Å °-0.0912884542755 Å °0.339954079842 Å °-0.0597858195779 Å °-0.163707658961 Å °
Refinement TLS groupSelection details: all

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