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- PDB-8frh: Apo structure of D59C mutant of a melibiose transporter -

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Basic information

Entry
Database: PDB / ID: 8frh
TitleApo structure of D59C mutant of a melibiose transporter
ComponentsMelibiose permease
KeywordsMEMBRANE PROTEIN / sugar transporter / Na-coupled MFS symporter
Function / homology
Function and homology information


: / symporter activity / sodium ion transport / carbohydrate transport / plasma membrane
Similarity search - Function
Sodium:galactoside symporter / Sodium:galactoside symporter, conserved site / Sodium:galactoside symporter family signature. / MFS/sugar transport protein / Lactose permease-like / MFS transporter superfamily
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsGuan, L. / Hariharan, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01GM122759 United States
CitationJournal: To Be Published
Title: Apo structure of D59C mutant of a melibiose transporter
Authors: Guan, L. / Hariharan, P.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: 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)54,3312
Polymers54,0921
Non-polymers2381
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-2 kcal/mol
Surface area19260 Å2
Unit cell
Length a, b, c (Å)127.930, 127.930, 104.522
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / Gene: melB, STM4299 / 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
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: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, pH 8.5 100 mm NaCl 50 mM CaCL2 32% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→20 Å / Num. obs: 16869 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21.8 % / CC1/2: 1 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.037 / Χ2: 1.3 / Net I/σ(I): 21.2
Reflection shellResolution: 3.18→3.27 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 21.2 / Num. unique obs: 16869 / CC1/2: 0.436 / Rpim(I) all: 0.451 / Rrim(I) all: 0.156 / Χ2: 1.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIXdev_3936refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→19.91 Å / SU ML: 0.5017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2863 1672 9.91 %
Rwork0.26 15197 -
obs0.2626 16869 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.05 Å2
Refinement stepCycle: LAST / Resolution: 3.18→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 16 0 3577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273669
X-RAY DIFFRACTIONf_angle_d0.51064988
X-RAY DIFFRACTIONf_chiral_restr0.0368584
X-RAY DIFFRACTIONf_plane_restr0.0033602
X-RAY DIFFRACTIONf_dihedral_angle_d7.2239503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.270.36731340.38441242X-RAY DIFFRACTION99.85
3.27-3.380.38081330.36191249X-RAY DIFFRACTION100
3.38-3.50.36721400.32191263X-RAY DIFFRACTION100
3.5-3.640.31391340.31461254X-RAY DIFFRACTION99.93
3.64-3.80.2851350.28951228X-RAY DIFFRACTION100
3.8-40.25221380.26661278X-RAY DIFFRACTION100
4-4.250.32631390.27711249X-RAY DIFFRACTION100
4.25-4.570.27411480.25951277X-RAY DIFFRACTION100
4.57-5.030.26071390.24131255X-RAY DIFFRACTION100
5.03-5.740.3031430.26171277X-RAY DIFFRACTION100
5.74-7.170.29591420.28191293X-RAY DIFFRACTION100
7.18-19.910.25641470.21161332X-RAY DIFFRACTION99.33
Refinement TLS params.Method: refined / Origin x: -25.2442813874 Å / Origin y: 50.8654464875 Å / Origin z: -6.22304196232 Å
111213212223313233
T0.483439776164 Å2-0.0748263652032 Å20.072903418218 Å2-1.02795168704 Å20.0120340273687 Å2--1.02865449018 Å2
L3.56630865698 °21.29564219718 °20.00887339325764 °2-2.691321201 °2-0.181431169751 °2--2.75010362086 °2
S0.381004121285 Å °0.38710851217 Å °0.152490981934 Å °0.144675449484 Å °-0.226201829153 Å °0.0452250654034 Å °0.163708363164 Å °-0.0452845058968 Å °-0.161028088964 Å °
Refinement TLS groupSelection details: all

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