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- PDB-3f4j: Crystal structure of LeuT bound to glycine and sodium -

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Basic information

Entry
Database: PDB / ID: 3f4j
TitleCrystal structure of LeuT bound to glycine and sodium
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / membrane protein / NSS / SLC6 / sodium-coupled / 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 / GLYCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 a Na(+)/Cl(-)-dependent neurotransmitter transporter
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

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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)59,3688
Polymers58,0771
Non-polymers1,2917
Water1,45981
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,73616
Polymers116,1552
Non-polymers2,58114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5150 Å2
ΔGint-24 kcal/mol
Surface area38440 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.060, 86.550, 81.450
Angle α, β, γ (deg.)90.00, 95.27, 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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#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.: 4 / Source method: obtained synthetically / 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.: 81 / 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: 54.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.4M NaCl, 24-26% 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 33833 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.51 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 30
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3083 / % possible all: 90.3

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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: 2.15→47.94 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1786 5.34 %RANDOM
Rwork0.2035 ---
obs0.2047 33470 98.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.752 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 50.25 Å2
Baniso -1Baniso -2Baniso -3
1-22.3314 Å20 Å28.0571 Å2
2---12.7187 Å20 Å2
3----9.6127 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 76 81 4206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.721
X-RAY DIFFRACTIONf_dihedral_angle_d16.838
X-RAY DIFFRACTIONf_plane_restr0.003
X-RAY DIFFRACTIONf_chiral_restr0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20820.29081540.28982174X-RAY DIFFRACTION90
2.2082-2.27310.2491450.26182307X-RAY DIFFRACTION95
2.2731-2.34650.23131630.23922409X-RAY DIFFRACTION99
2.3465-2.43040.27611300.21352462X-RAY DIFFRACTION100
2.4304-2.52770.24621250.20212475X-RAY DIFFRACTION100
2.5277-2.64270.20941100.18962484X-RAY DIFFRACTION100
2.6427-2.7820.24331260.18612459X-RAY DIFFRACTION100
2.782-2.95630.1891220.18792493X-RAY DIFFRACTION100
2.9563-3.18450.23471600.19722436X-RAY DIFFRACTION100
3.1845-3.50490.20821450.19182474X-RAY DIFFRACTION100
3.5049-4.01180.20431400.1842469X-RAY DIFFRACTION100
4.0118-5.05360.1881320.18412503X-RAY DIFFRACTION100
5.0536-47.95210.2541340.22272539X-RAY DIFFRACTION100

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