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- PDB-3f3c: Crystal structure of LeuT bound to 4-Fluoro-L-Phenylalanine and sodium -

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Basic information

Entry
Database: PDB / ID: 3f3c
TitleCrystal structure of LeuT bound to 4-Fluoro-L-Phenylalanine 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 / 4-FLUORO-L-PHENYLALANINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 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 1.3Sep 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)59,7689
Polymers58,0771
Non-polymers1,6918
Water1,58588
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,53718
Polymers116,1552
Non-polymers3,38216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6050 Å2
ΔGint-9 kcal/mol
Surface area38750 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.120, 86.322, 81.579
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-588-

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-PFF / 4-FLUORO-L-PHENYLALANINE


Type: L-peptide linking / Mass: 183.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10FNO2
#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.: 88 / 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: 54.79 %
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: Jan 17, 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: 2.1→62.3 Å / Num. obs: 33636 / % possible obs: 92.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2311 / % possible all: 64.3

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Processing

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

2a65


Resolution: 2.1→47.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.748 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23744 1694 5 %RANDOM
Rwork0.19564 ---
obs0.19772 31935 92.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.192 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å20 Å21.2 Å2
2---2.04 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 115 88 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224317
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9745877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5115519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91521.975162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0381520
X-RAY DIFFRACTIONr_chiral_restr0.060.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023161
X-RAY DIFFRACTIONr_nbd_refined0.2140.32264
X-RAY DIFFRACTIONr_nbtor_refined0.330.53091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5292
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.58
X-RAY DIFFRACTIONr_mcbond_it1.2123.52546
X-RAY DIFFRACTIONr_mcangle_it1.9514.54112
X-RAY DIFFRACTIONr_scbond_it1.1693.51869
X-RAY DIFFRACTIONr_scangle_it1.6934.51759
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 82 -
Rwork0.239 1597 -
obs-1679 62.12 %

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