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- PDB-3f4i: Crystal Structure of LeuT bound to L-selenomethionine and sodium -

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Basic information

Entry
Database: PDB / ID: 3f4i
TitleCrystal Structure of LeuT bound to L-selenomethionine and sodium
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / membrane protein / SLC6 / NSS / sodium-couple / neurotransmitter / transporter / Symport / Transmembrane / Transport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / SELENOMETHIONINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSingh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E.
Citation
Journal: Science / Year: 2008
Title: A competitive inhibitor traps LeuT in an open-to-out conformation.
Authors: Singh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E.
#1: Journal: Nature / Year: 2007
Title: Antidepressant binding site in a bacterial homologue of neurotransmitter transporters
Authors: Singh, S.K. / Yamashita, A. / Gouaux, E.
#2: Journal: Nature / Year: 2005
Title: Crystal structure of a bacterial homologue of Na(+)/Cl(-)-dependent neurotransmitter transporters
Authors: Yamashita, A. / Singh, S.K. / Kawate, T. / Jin, Y. / Gouaux, E.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7819
Polymers58,0771
Non-polymers1,7048
Water2,018112
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,56318
Polymers116,1552
Non-polymers3,40816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5520 Å2
ΔGint-11 kcal/mol
Surface area39780 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.777, 86.703, 81.692
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter / leucine transporter


Mass: 58077.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: snf, aq_2077 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O67854
#2: Chemical ChemComp-MSE / SELENOMETHIONINE


Type: L-peptide linking / Mass: 196.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2Se
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.2M NaCl, 17-22% PEG-MME 550, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→81.38 Å / Num. obs: 45123 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A65

2a65


Resolution: 1.95→31.105 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 2527 5.61 %
Rwork0.1922 --
obs0.1936 45065 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.453 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 39.43 Å2
Baniso -1Baniso -2Baniso -3
1-13.2641 Å20 Å2-0.7083 Å2
2---7.0537 Å20 Å2
3----6.2104 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 111 112 4268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034280
X-RAY DIFFRACTIONf_angle_d0.7295817
X-RAY DIFFRACTIONf_dihedral_angle_d16.3291490
X-RAY DIFFRACTIONf_chiral_restr0.051666
X-RAY DIFFRACTIONf_plane_restr0.004696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98750.28551420.27332207X-RAY DIFFRACTION96
1.9875-2.02810.251510.22472341X-RAY DIFFRACTION99
2.0281-2.07220.23141680.21352301X-RAY DIFFRACTION99
2.0722-2.12040.21331850.19962298X-RAY DIFFRACTION99
2.1204-2.17340.20571560.18552358X-RAY DIFFRACTION99
2.1734-2.23210.18151460.18242364X-RAY DIFFRACTION99
2.2321-2.29780.20811640.17732338X-RAY DIFFRACTION99
2.2978-2.37190.17661430.17172325X-RAY DIFFRACTION99
2.3719-2.45670.20091180.16352385X-RAY DIFFRACTION100
2.4567-2.5550.18471140.16812404X-RAY DIFFRACTION100
2.555-2.67120.19641160.16922405X-RAY DIFFRACTION100
2.6712-2.81190.21791130.17672413X-RAY DIFFRACTION100
2.8119-2.9880.23581260.18172392X-RAY DIFFRACTION100
2.988-3.21850.19611500.19132367X-RAY DIFFRACTION100
3.2185-3.5420.20261480.19032381X-RAY DIFFRACTION100
3.542-4.05350.20891330.18532401X-RAY DIFFRACTION100
4.0535-5.10340.1891230.17962433X-RAY DIFFRACTION100
5.1034-31.10870.25151310.20992425X-RAY DIFFRACTION99

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