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- PDB-3f3e: Crystal structure of LeuT bound to L-leucine (30 mM) and sodium -

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Basic information

Entry
Database: PDB / ID: 3f3e
TitleCrystal structure of LeuT bound to L-leucine (30 mM) and sodium
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / SLC6 / NSS / transmembrane / sodium-coupled / transporter / Symport / Transport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / LEUCINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSingh, S.K. / Piscitelli, C.L. / Yamashita, A. / Gouaux, E.
CitationJournal: 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.
History
DepositionOct 30, 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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)60,30111
Polymers58,0771
Non-polymers2,22410
Water2,756153
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,60222
Polymers116,1552
Non-polymers4,44720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7960 Å2
ΔGint9 kcal/mol
Surface area38640 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.361, 86.664, 81.382
Angle α, β, γ (deg.)90.00, 95.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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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-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#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.: 7
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.: 153 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 56738 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5614 / % possible all: 98.1

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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: 1.8→44.44 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2877 5.07 %RANDOM
Rwork0.1795 ---
obs0.1808 56694 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.212 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 37.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 145 153 4342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.244
X-RAY DIFFRACTIONf_dihedral_angle_d17.273
X-RAY DIFFRACTIONf_plane_restr0.006
X-RAY DIFFRACTIONf_chiral_restr0.084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82670.27321480.24612427X-RAY DIFFRACTION93
1.8267-1.85820.26071380.22272493X-RAY DIFFRACTION98
1.8582-1.8920.25531330.2062562X-RAY DIFFRACTION98
1.892-1.92840.2621300.20382535X-RAY DIFFRACTION98
1.9284-1.96770.22211310.19252539X-RAY DIFFRACTION98
1.9677-2.01050.20581450.18122549X-RAY DIFFRACTION99
2.0105-2.05730.20191280.17262528X-RAY DIFFRACTION99
2.0573-2.10870.20861290.16962562X-RAY DIFFRACTION99
2.1087-2.16570.22031380.162578X-RAY DIFFRACTION99
2.1657-2.22950.21151150.16272594X-RAY DIFFRACTION99
2.2295-2.30140.21341450.16112544X-RAY DIFFRACTION99
2.3014-2.38370.18451550.15852546X-RAY DIFFRACTION99
2.3837-2.47910.1761240.15742595X-RAY DIFFRACTION99
2.4791-2.59190.18371490.16412570X-RAY DIFFRACTION99
2.5919-2.72860.22791360.16542561X-RAY DIFFRACTION99
2.7286-2.89950.21561340.16882583X-RAY DIFFRACTION100
2.8995-3.12330.20811350.17312620X-RAY DIFFRACTION100
3.1233-3.43750.19061310.17372600X-RAY DIFFRACTION100
3.4375-3.93470.19221460.16562604X-RAY DIFFRACTION100
3.9347-4.95620.17441390.17372610X-RAY DIFFRACTION100
4.9562-44.45380.21761480.20352617X-RAY DIFFRACTION98

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