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- PDB-3f3d: Crystal structure of LeuT bound to L-Methionine and sodium -

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Basic information

Entry
Database: PDB / ID: 3f3d
TitleCrystal structure of LeuT bound to L-Methionine and sodium
ComponentsTransporterTransport protein
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 / membrane / METHIONINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 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)59,7349
Polymers58,0771
Non-polymers1,6578
Water95553
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,46918
Polymers116,1552
Non-polymers3,31416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5550 Å2
ΔGint-13 kcal/mol
Surface area39640 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.333, 86.636, 81.166
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter / Transport protein / 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: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
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: 1.7712 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 2006
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.3→47.51 Å / Num. obs: 23640 / % possible obs: 87.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1444 / % possible all: 53.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A65

2a65


Resolution: 2.3→43.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.01 / SU ML: 0.149 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22419 1178 5 %RANDOM
Rwork0.19724 ---
obs0.19862 22446 87.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.166 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å2-1.43 Å2
2---0.87 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 111 53 4208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224280
X-RAY DIFFRACTIONr_angle_refined_deg0.971.9725817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4175507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57722.086163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6741520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023130
X-RAY DIFFRACTIONr_nbd_refined0.1880.22087
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2132
X-RAY DIFFRACTIONr_metal_ion_refined0.1970.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.25
X-RAY DIFFRACTIONr_mcbond_it0.4381.52528
X-RAY DIFFRACTIONr_mcangle_it0.81324075
X-RAY DIFFRACTIONr_scbond_it0.79531849
X-RAY DIFFRACTIONr_scangle_it1.3414.51742
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 40 -
Rwork0.26 905 -
obs-945 47.87 %

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