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- PDB-3gwv: Leucine transporter LeuT in complex with R-fluoxetine -

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Basic information

Entry
Database: PDB / ID: 3gwv
TitleLeucine transporter LeuT in complex with R-fluoxetine
ComponentsTransporterTransport protein
KeywordsTRANSPORT PROTEIN / NEUROTRANSMITTER / TRANSMEMBRANE TRANSPORT / INTEGRAL MEMBRANE PROTEIN / ANTIDEPRESSANT / NSS / Symport / Transmembrane / Transport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / LEUCINE / Chem-RFX / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhou, Z. / Zhen, J. / Karpowich, N.K. / Law, C.J. / Reith, M.E.A. / Wang, D.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Antidepressant specificity of serotonin transporter suggested by three LeuT-SSRI structures.
Authors: Zhou, Z. / Zhen, J. / Karpowich, N.K. / Law, C.J. / Reith, M.E. / Wang, D.N.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0975
Polymers57,6111
Non-polymers4864
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,19510
Polymers115,2222
Non-polymers9738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2460 Å2
ΔGint-32 kcal/mol
Surface area36120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.813, 87.390, 81.154
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transporter / Transport protein


Mass: 57610.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_2077, LeuT, snf / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: O67854
#2: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-RFX / (3R)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine / Fluoxetine / Fluoxetine


Mass: 309.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18F3NO / Comment: antidepressant, inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG550 MME, NACL, pH 7, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.35→47.5 Å / Num. obs: 23383 / % possible obs: 91.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Χ2: 0.834 / Net I/σ(I): 15.564
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.431.60.21216380.606165.5
2.43-2.531.80.21419450.586176.1
2.53-2.652.10.1921420.631184.7
2.65-2.792.50.17623760.551193.8
2.79-2.9630.16924960.573198.8
2.96-3.193.50.14425320.571199.8
3.19-3.513.70.125550.711199.9
3.51-4.023.70.06825361.132199.9
4.02-5.063.70.04425721.19199.9
5.06-503.70.03125911.038199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A65

2a65


Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.38 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1188 5.1 %RANDOM
Rwork0.201 ---
obs0.203 23379 91.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.21 Å2 / Biso mean: 38.408 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å2-0.95 Å2
2---0.9 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 33 70 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224119
X-RAY DIFFRACTIONr_angle_refined_deg1.0081.9535609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5545495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85121.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1315633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9221520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023077
X-RAY DIFFRACTIONr_nbd_refined0.1940.22078
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.1860.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.24
X-RAY DIFFRACTIONr_mcbond_it0.4461.52471
X-RAY DIFFRACTIONr_mcangle_it0.82323981
X-RAY DIFFRACTIONr_scbond_it0.91631746
X-RAY DIFFRACTIONr_scangle_it1.4584.51628
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 58 -
Rwork0.191 1098 -
all-1156 -
obs--62.05 %

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