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- PDB-9oli: Crystal structure of the melibiose-bound melibiose transporter -

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Basic information

Entry
Database: PDB / ID: 9oli
TitleCrystal structure of the melibiose-bound melibiose transporter
ComponentsMelibiose permease
KeywordsMEMBRANE PROTEIN / melibiose binding / MFS
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
alpha-melibiose / Melibiose permease
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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
CitationJournal: 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

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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)54,4352
Polymers54,0921
Non-polymers3421
Water362
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)126.421, 126.421, 103.555
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 (bacteria)
Strain: LT2 / Gene: melB, STM4299 / Organ: Salmonella typhimurium / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / References: UniProt: P30878
#2: Polysaccharide alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 4.61 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, NaCl, 100 mM, CaCl, 50 mM, PEG400, 34%
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→20 Å / Num. obs: 18439 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 122.25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Net I/σ(I): 11.8
Reflection shellResolution: 3.05→3.26 Å / Num. unique obs: 18439 / CC1/2: 1 / % possible all: 99.5

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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: 3.05→19.7 Å / SU ML: 0.5421 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2937 1784 9.68 %
Rwork0.2551 16655 -
obs0.2589 18439 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 135.7 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 23 2 3540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253631
X-RAY DIFFRACTIONf_angle_d0.54534950
X-RAY DIFFRACTIONf_chiral_restr0.0377589
X-RAY DIFFRACTIONf_plane_restr0.0036596
X-RAY DIFFRACTIONf_dihedral_angle_d12.17891271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.36751360.35621274X-RAY DIFFRACTION99.51
3.13-3.220.36651380.31921265X-RAY DIFFRACTION99.93
3.22-3.330.3541390.32131273X-RAY DIFFRACTION100
3.33-3.450.37261330.33371238X-RAY DIFFRACTION100
3.45-3.580.38151390.29641279X-RAY DIFFRACTION100
3.58-3.750.40871300.31641257X-RAY DIFFRACTION98.51
3.75-3.940.34491390.27621275X-RAY DIFFRACTION99.72
3.94-4.190.30691330.24131295X-RAY DIFFRACTION99.93
4.19-4.50.26021350.21491269X-RAY DIFFRACTION99.72
4.51-4.950.25531380.24041292X-RAY DIFFRACTION99.93
4.95-5.650.2921360.26111297X-RAY DIFFRACTION99.93
5.66-7.070.31311450.31031301X-RAY DIFFRACTION99.66
7.08-19.70.25871430.21431340X-RAY DIFFRACTION98.41
Refinement TLS params.Method: refined / Origin x: -55.9359216611 Å / Origin y: 3.69565166002 Å / Origin z: 11.1606995028 Å
111213212223313233
T1.23601676626 Å2-0.223899095077 Å20.029808577758 Å2-0.612722629402 Å20.0282548418116 Å2--1.43960561629 Å2
L1.92214363612 °20.274149458886 °2-0.316618109913 °2-4.09936124273 °2-0.0676353327526 °2--2.47666645653 °2
S-0.210602417255 Å °0.155962402987 Å °0.057733376535 Å °0.133330151578 Å °0.341827042186 Å °-0.0421892043192 Å °0.272878217644 Å °0.123356275951 Å °-0.158720587887 Å °
Refinement TLS groupSelection details: all

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