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- PDB-3f3a: Crystal Structure of LeuT bound to L-Tryptophan and Sodium -

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Basic information

Entry
Database: PDB / ID: 3f3a
TitleCrystal Structure of LeuT bound to L-Tryptophan and Sodium
ComponentsTransporter
KeywordsTRANSPORT PROTEIN / SLC6 / NSS / transmembrane / sodium-coupled / transporter / Symport
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / plasma membrane / TETRADECANE / TRYPTOPHAN / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: 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 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,18515
Polymers58,0771
Non-polymers3,10814
Water1,820101
1
A: Transporter
hetero molecules

A: Transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,37130
Polymers116,1552
Non-polymers6,21628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area8280 Å2
ΔGint-15 kcal/mol
Surface area38650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.566, 85.218, 82.274
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

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Components

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Protein / Sugars , 2 types, 8 molecules A

#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
#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

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Non-polymers , 4 types, 108 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.4M 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: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2007
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 41152 / % possible obs: 97.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 31.79 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.1 / Num. unique all: 3834 / % possible all: 90.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2A65

2a65


Resolution: 2→48.232 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2040 5.06 %RANDOM
Rwork0.1981 ---
obs0.1997 40334 97.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 41.97 Å2
Refinement stepCycle: LAST / Resolution: 2→48.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 216 101 4327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.049
X-RAY DIFFRACTIONf_dihedral_angle_d18.628
X-RAY DIFFRACTIONf_plane_restr0.005
X-RAY DIFFRACTIONf_chiral_restr0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.32951170.29452440X-RAY DIFFRACTION91
2.0465-2.09770.33041480.28542459X-RAY DIFFRACTION97
2.0977-2.15440.30941350.25852567X-RAY DIFFRACTION98
2.1544-2.21780.28231400.23782563X-RAY DIFFRACTION99
2.2178-2.28940.26641240.21662597X-RAY DIFFRACTION99
2.2894-2.37120.26281410.20162563X-RAY DIFFRACTION99
2.3712-2.46620.24641380.19342551X-RAY DIFFRACTION98
2.4662-2.57840.24181430.18472550X-RAY DIFFRACTION99
2.5784-2.71430.21211470.18592554X-RAY DIFFRACTION99
2.7143-2.88440.24081230.18322580X-RAY DIFFRACTION98
2.8844-3.1070.24391360.18672581X-RAY DIFFRACTION99
3.107-3.41960.22871390.18392605X-RAY DIFFRACTION99
3.4196-3.91430.2131280.17442554X-RAY DIFFRACTION98
3.9143-4.93080.16291400.17352544X-RAY DIFFRACTION96
4.9308-48.24610.22481410.20992586X-RAY DIFFRACTION96

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