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- PDB-9olr: Crystal structure of D59C MelB st bound with alpha-methyl galacto... -

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Basic information

Entry
Database: PDB / ID: 9olr
TitleCrystal structure of D59C MelB st bound with alpha-methyl galactoside (aMG)
ComponentsMelibiose permease
KeywordsMEMBRANE PROTEIN / alpha methyl galactoside / sugar binding / MFS / symporter
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
methyl alpha-D-galactopyranoside / Melibiose permease
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.68 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)54,2872
Polymers54,0921
Non-polymers1941
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.496, 127.496, 106.039
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: Salmonella typhimurium / Gene: melB, STM4299 / Production host: Escherichia coli 0.1197 (bacteria) / References: UniProt: P30878
#2: Sugar ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
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: 4.6 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, CaCl2, 50 mM, PEG400, 33%
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: 0.979499 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: 0.979499 Å / Relative weight: 1
ReflectionResolution: 3.68→20 Å / Num. obs: 11026 / % possible obs: 99.8 % / Redundancy: 9.2 % / Biso Wilson estimate: 81.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.066 / Rrim(I) all: 0.145 / Net I/σ(I): 8.4
Reflection shellResolution: 3.68→4.11 Å / Redundancy: 8.8 % / Num. unique obs: 3102 / CC1/2: 0.933 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.68→19.91 Å / SU ML: 0.5813 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.1624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3307 547 4.98 %
Rwork0.2952 10434 -
obs0.2969 10981 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.76 Å2
Refinement stepCycle: LAST / Resolution: 3.68→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 13 0 3570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023663
X-RAY DIFFRACTIONf_angle_d0.4864988
X-RAY DIFFRACTIONf_chiral_restr0.035589
X-RAY DIFFRACTIONf_plane_restr0.0034602
X-RAY DIFFRACTIONf_dihedral_angle_d11.39531275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.050.59171090.52882562X-RAY DIFFRACTION98.74
4.05-4.630.3171690.29672553X-RAY DIFFRACTION100
4.63-5.80.33511280.2772620X-RAY DIFFRACTION99.89
5.81-19.910.26971410.22232699X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 24.98625698 Å / Origin y: -50.7525759057 Å / Origin z: -6.0962811753 Å
111213212223313233
T0.458195347584 Å2-0.0788656788429 Å2-0.08092353917 Å2-1.10746140936 Å20.0111835444327 Å2--1.20915247727 Å2
L3.10356034251 °20.990146159376 °20.0640529866376 °2-2.52977895767 °20.156634028812 °2--2.80246093621 °2
S0.352548126587 Å °0.46875082643 Å °-0.00220145027328 Å °0.0458836900311 Å °-0.0969984666712 Å °-0.0291051464426 Å °-0.111245099403 Å °0.0647774582683 Å °-0.216668618682 Å °
Refinement TLS groupSelection details: all

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