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- PDB-8fq9: Crystal structure of a ligand-bound cation-site mutant D55C of a ... -

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Basic information

Entry
Database: PDB / ID: 8fq9
TitleCrystal structure of a ligand-bound cation-site mutant D55C of a melibiose transporter
ComponentsMelibiose permease
KeywordsMEMBRANE PROTEIN / Cation-coupled symporter / sugar transporter / MFS Na+-coupled transporter
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
Chem-LMO / Melibiose permease
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122759 United States
Citation
Journal: J.Biol.Chem. / Year: 2024
Title: Distinct roles of the major binding residues in the cation-binding pocket of the melibiose transporter MelB.
Authors: Hariharan, P. / Bakhtiiari, A. / Liang, R. / Guan, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Zwart, P.H.
History
DepositionJan 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)54,8413
Polymers54,0921
Non-polymers7492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, cryoEM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-3 kcal/mol
Surface area19370 Å2
Unit cell
Length a, b, c (Å)127.225, 127.225, 104.042
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: D55C
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: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Sugar ChemComp-LMO / dodecyl 6-O-alpha-D-galactopyranosyl-beta-D-glucopyranoside / DDMB / dodecyl melibioside


Type: saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION
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: 6.5
Details: MES, 100 mM, PH 6.5 NaCl, 100 mM CaCl, 50 mM PEG400, 32%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 19790 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Χ2: 1.02 / Net I/σ(I): 16.8
Reflection shellResolution: 3.18→3.4 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1.705 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2982 / CC1/2: 0.728 / Rpim(I) all: 0.398 / Rrim(I) all: 1.791 / Χ2: 1.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3936refinement
PHENIXdev_3936refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.56 Å / SU ML: 0.4464 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2883 1960 9.9 %
Rwork0.263 17830 -
obs0.2655 19790 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.73 Å2
Refinement stepCycle: LAST / Resolution: 3→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 41 0 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233711
X-RAY DIFFRACTIONf_angle_d0.5575049
X-RAY DIFFRACTIONf_chiral_restr0.0365596
X-RAY DIFFRACTIONf_plane_restr0.003606
X-RAY DIFFRACTIONf_dihedral_angle_d5.4981507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.37611200.3591245X-RAY DIFFRACTION99.71
3.08-3.160.35761480.35911277X-RAY DIFFRACTION99.86
3.16-3.250.37921350.35911251X-RAY DIFFRACTION100
3.25-3.350.36141430.34381275X-RAY DIFFRACTION99.93
3.36-3.470.32511380.30321245X-RAY DIFFRACTION100
3.48-3.610.31561390.29491248X-RAY DIFFRACTION100
3.61-3.780.28971420.28791256X-RAY DIFFRACTION100
3.78-3.980.31041410.27251270X-RAY DIFFRACTION100
3.98-4.220.30221400.26971269X-RAY DIFFRACTION100
4.22-4.550.27641400.26021293X-RAY DIFFRACTION100
4.55-50.26121380.2471270X-RAY DIFFRACTION100
5-5.720.28811450.26451277X-RAY DIFFRACTION100
5.72-7.170.31371460.29171309X-RAY DIFFRACTION100
7.18-24.560.24831450.20941345X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: -56.3807391713 Å / Origin y: 3.82089233665 Å / Origin z: 11.1438046751 Å
111213212223313233
T1.0883967816 Å2-0.218526540117 Å2-0.000957210847134 Å2-0.603952122324 Å20.0556849475309 Å2--1.05375163493 Å2
L1.03941641258 °2-0.0624259555431 °2-0.0351150597879 °2-3.14758766141 °20.788813486246 °2--2.56122913549 °2
S-0.109685879294 Å °0.181967053205 Å °0.0492374791632 Å °0.162811480903 Å °0.348543963359 Å °0.118936689859 Å °0.0601416879446 Å °0.126725987107 Å °-0.239422338987 Å °
Refinement TLS groupSelection details: all

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