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- PDB-7lqj: Crystal structure of LeuT bound to L-Alanine -

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Basic information

Entry
Database: PDB / ID: 7lqj
TitleCrystal structure of LeuT bound to L-Alanine
ComponentsNa(+):neurotransmitter symporter (Snf family)
KeywordsTRANSPORT PROTEIN / Transporter / Leucine transporter
Function / homologySodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / sodium ion transmembrane transport / membrane / ALANINE / Na(+):neurotransmitter symporter (Snf family)
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 Å
AuthorsFont, J. / Aguilar, J. / Galli, A. / Ryan, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01-DA038058 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01-DA035263 United States
CitationJournal: Elife / Year: 2021
Title: Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia.
Authors: Aguilar, J.I. / Cheng, M.H. / Font, J. / Schwartz, A.C. / Ledwitch, K. / Duran, A. / Mabry, S.J. / Belovich, A.N. / Zhu, Y. / Carter, A.M. / Shi, L. / Kurian, M.A. / Fenollar-Ferrer, C. / ...Authors: Aguilar, J.I. / Cheng, M.H. / Font, J. / Schwartz, A.C. / Ledwitch, K. / Duran, A. / Mabry, S.J. / Belovich, A.N. / Zhu, Y. / Carter, A.M. / Shi, L. / Kurian, M.A. / Fenollar-Ferrer, C. / Meiler, J. / Ryan, R.M. / Mchaourab, H.S. / Bahar, I. / Matthies, H.J. / Galli, A.
History
DepositionFeb 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6749
Polymers58,0771
Non-polymers1,5978
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules

A: Na(+):neurotransmitter symporter (Snf family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,34918
Polymers116,1552
Non-polymers3,19416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.484, 86.866, 81.145
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Na(+):neurotransmitter symporter (Snf family)


Mass: 58077.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: snf, aq_2077 / Production host: Escherichia coli (E. coli) / References: UniProt: O67854
#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: 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: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 53.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes/NaOH pH 7.0, 200 mM NaCl, 20-22% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.14→43.992 Å / Num. obs: 33365 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 14.9
Reflection shellResolution: 2.14→2.21 Å / Num. unique obs: 2552 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f3e

3f3e


Resolution: 2.144→43.992 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1780 5.34 %RANDOM
Rwork0.1667 31569 --
obs0.1682 33349 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 47.7454 Å2 / Biso min: 25.67 Å2
Refinement stepCycle: final / Resolution: 2.144→43.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 99 135 4247
Biso mean--81.67 57.94 -
Num. residues----505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.144-2.20150.25871110.2218226693
2.2015-2.26630.23351320.1852420100
2.2663-2.33950.20811470.17342444100
2.3395-2.42310.20541440.1682407100
2.4231-2.52010.21511750.15642406100
2.5201-2.63480.18261450.15392426100
2.6348-2.77360.16441610.14762386100
2.7736-2.94740.21031270.14962474100
2.9474-3.17490.20391240.15662439100
3.1749-3.49430.1691420.16022447100
3.4943-3.99960.23141210.16252451100
3.9996-5.0380.16811190.1612493100
5.038-43.9920.20031320.18632510100
Refinement TLS params.Method: refined / Origin x: -17.5075 Å / Origin y: -14.0658 Å / Origin z: 21.4846 Å
111213212223313233
T0.2899 Å20.0231 Å2-0.0101 Å2-0.302 Å20.0176 Å2--0.2477 Å2
L1.1042 °2-0.1315 °20.1155 °2-1.3504 °20.2648 °2--1.2036 °2
S-0.0492 Å °0.0572 Å °0.019 Å °0.0085 Å °0.002 Å °0.174 Å °-0.0547 Å °-0.0729 Å °0.0491 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 511
2X-RAY DIFFRACTION1allA801
3X-RAY DIFFRACTION1allA901 - 1501
4X-RAY DIFFRACTION1allS2 - 138

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