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- PDB-7l17: Crystal structure of sugar-bound melibiose permease MelB -

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Basic information

Entry
Database: PDB / ID: 7l17
TitleCrystal structure of sugar-bound melibiose permease MelB
ComponentsMelibiose carrier protein
KeywordsTRANSPORT PROTEIN / MFS-fold / galactoside binding / secondary active transport / MelB
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
4-nitrophenyl alpha-D-galactopyranoside / Melibiose permease
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsGuan, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122759 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS105863 United States
CitationJournal: Commun Biol / Year: 2021
Title: X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB.
Authors: Guan, L. / Hariharan, P.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melibiose carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3942
Polymers54,0921
Non-polymers3011
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.364, 126.364, 104.334
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 carrier protein / Melibiose permease / Melibiose transporter / Na+ (Li+)/melibiose symporter / Thiomethylgalactoside permease II


Mass: 54092.496 Da / Num. of mol.: 1 / Mutation: D59C, L5M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: melB, STM4299 / Plasmid: pK95 / Details (production host): A 10xHis tag on the C-terminus / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / Variant (production host): melBlacYZ / References: UniProt: P30878
#2: Sugar ChemComp-9PG / 4-nitrophenyl alpha-D-galactopyranoside / 4-nitrophenyl alpha-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO8 / Feature type: SUBJECT OF INVESTIGATION
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: 4.76 Å3/Da / Density % sol: 74.18 % / Description: Rod
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM BaCl2, 50 mM CaCl2, 100 mM Tris-HCl, pH 8.5, and 29-32% PEG 400, 6 mM a-NPG
PH range: 6.5 - 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: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.05→29.8945 Å / Num. obs: 18680 / % possible obs: 99.6949 % / Redundancy: 21 % / Biso Wilson estimate: 98.33 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Χ2: 0.99 / Net I/σ(I): 20.5
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 22.5 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3342 / CC1/2: 0.3 / Rpim(I) all: 0.419 / Rrim(I) all: 1.43 / Χ2: 0.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_3936refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→29.89 Å / SU ML: 0.4151 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.9663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2935 1856 9.97 %
Rwork0.2594 16761 -
obs0.2627 18617 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.02 Å2
Refinement stepCycle: LAST / Resolution: 3.05→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 21 0 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263676
X-RAY DIFFRACTIONf_angle_d0.5365005
X-RAY DIFFRACTIONf_chiral_restr0.0363589
X-RAY DIFFRACTIONf_plane_restr0.0035604
X-RAY DIFFRACTIONf_dihedral_angle_d4.096495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.33831430.35571265X-RAY DIFFRACTION99.93
3.13-3.220.36391370.31571284X-RAY DIFFRACTION100
3.22-3.330.33481480.29371283X-RAY DIFFRACTION100
3.33-3.450.32411330.30041263X-RAY DIFFRACTION99.93
3.45-3.590.32231440.28531282X-RAY DIFFRACTION100
3.59-3.750.35051410.30911272X-RAY DIFFRACTION99.09
3.75-3.950.3241360.2871266X-RAY DIFFRACTION98.8
3.95-4.190.33141500.27771284X-RAY DIFFRACTION99.72
4.19-4.510.27921420.24771284X-RAY DIFFRACTION99.51
4.52-4.970.25391470.2411300X-RAY DIFFRACTION99.59
4.97-5.680.29891440.25941283X-RAY DIFFRACTION99.79
5.68-7.140.31641420.27591329X-RAY DIFFRACTION99.93
7.14-29.890.24821490.21661366X-RAY DIFFRACTION99.34
Refinement TLS params.Method: refined / Origin x: -24.7770580329 Å / Origin y: 50.363905649 Å / Origin z: -6.07337252499 Å
111213212223313233
T0.356228095473 Å2-0.104894036081 Å20.0640302869461 Å2-0.995898238833 Å20.0371850533011 Å2--1.00987279982 Å2
L2.63857678814 °20.426145139453 °20.55299810998 °2-2.31584210143 °20.571870637319 °2--2.71200707003 °2
S0.335700094495 Å °0.373996800362 Å °0.0657888005257 Å °0.0618956459249 Å °-0.126523005667 Å °0.0520825941606 Å °0.140614686719 Å °0.0766022222994 Å °-0.196670795075 Å °
Refinement TLS groupSelection details: all

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