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- PDB-4m64: 3D crystal structure of Na+/melibiose symporter of Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 4m64
Title3D crystal structure of Na+/melibiose symporter of Salmonella typhimurium
ComponentsMelibiose carrier protein
KeywordsTRANSPORT PROTEIN / melibiose permease / melibiose/Na+ symport / membrane transport protein / membrane carrier / glycoside-pentoside-hexuronide:cation symporter family / major facilitator superfamily / secondary active transport
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. / Lactose permease-like / MFS/sugar transport protein / MFS transporter superfamily
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsEthayathulla, A.S. / Guan, L.
CitationJournal: Nat Commun / Year: 2014
Title: Structure-based mechanism for Na(+)/melibiose symport by MelB.
Authors: Ethayathulla, A.S. / Yousef, M.S. / Amin, A. / Leblanc, G. / Kaback, H.R. / Guan, L.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melibiose carrier protein
B: Melibiose carrier protein
C: Melibiose carrier protein
D: Melibiose carrier protein


Theoretical massNumber of molelcules
Total (without water)216,9434
Polymers216,9434
Non-polymers00
Water00
1
A: Melibiose carrier protein


Theoretical massNumber of molelcules
Total (without water)54,2361
Polymers54,2361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Melibiose carrier protein


Theoretical massNumber of molelcules
Total (without water)54,2361
Polymers54,2361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Melibiose carrier protein


Theoretical massNumber of molelcules
Total (without water)54,2361
Polymers54,2361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Melibiose carrier protein


Theoretical massNumber of molelcules
Total (without water)54,2361
Polymers54,2361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.206, 127.206, 206.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Melibiose carrier protein / Melibiose permease / Melibiose transporter / Na+ (Li+)/melibiose symporter / Thiomethylgalactoside permease II


Mass: 54235.633 Da / Num. of mol.: 4 / Mutation: L5M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: melB, STM4299 / Plasmid: pK95 / Production host: Escherichia coli (E. coli) / References: UniProt: P30878

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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: 4.44 Å3/Da / Density % sol: 72.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.1M NaCl, 0.05M CaCl2, 32% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012 / Details: MIRROR
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 3.35→40 Å / Num. all: 99230 / Num. obs: 52990 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.52 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Threading Model of MelBst on FucP

Resolution: 3.35→38.64 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.822 / SU B: 48.125 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35945 2712 5.1 %RANDOM
Rwork0.31189 ---
obs0.31422 50526 99.38 %-
all-52990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.708 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0 Å2-0 Å2
2---1 Å2-0 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 3.35→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12982 0 0 0 12982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213316
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212895
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.95318160
X-RAY DIFFRACTIONr_angle_other_deg1.048329344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6551679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57622.363474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.505152026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4391550
X-RAY DIFFRACTIONr_chiral_restr0.0970.22162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214869
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.1029.396740
X-RAY DIFFRACTIONr_mcbond_other8.1029.396739
X-RAY DIFFRACTIONr_mcangle_it13.78614.0648411
X-RAY DIFFRACTIONr_mcangle_other13.29313.6768395
X-RAY DIFFRACTIONr_scbond_it6.2589.326576
X-RAY DIFFRACTIONr_scbond_other5.8269.0336575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.29613.5379744
X-RAY DIFFRACTIONr_long_range_B_refined29.86483.0555140
X-RAY DIFFRACTIONr_long_range_B_other29.86483.05155141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.35→3.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 182 -
Rwork0.191 3557 -
obs--93.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0852-0.06-0.10920.04390.07330.1522-0.0030.0174-0.01320.0068-0.0170.0051-0.0091-0.00720.020.0199-0.0126-0.00560.0233-0.00270.055-29.3989-48.1309106.7358
20.00350.006-0.00580.0174-0.0140.01220.0070.0037-0.00610.0144-0.0086-0.0026-0.01540.00130.00160.03010.0149-0.0190.0484-0.03840.0369-26.1346-48.456757.5525
30.06310.05240.020.05030.03170.0414-0.005-0.01220.0115-0.0082-0.00760.0147-0.01220.01560.01270.02010.0119-0.01320.03690.00590.0448-29.5376-48.11715.3419
40.08210.0808-0.06210.0862-0.05640.05050.00270.0058-0.01690.0007-0.0157-0.0117-0.0087-0.01740.0130.02490.0161-0.02780.0491-0.01580.0324-26.5765-47.883-43.675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 448
2X-RAY DIFFRACTION2B1 - 449
3X-RAY DIFFRACTION3C1 - 431
4X-RAY DIFFRACTION4D1 - 430

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