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- PDB-7lqk: Crystal structure of the R375A mutant of LeuT -

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Basic information

Entry
Database: PDB / ID: 7lqk
TitleCrystal structure of the R375A mutant of LeuT
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: 2.1 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)59,5889
Polymers57,9911
Non-polymers1,5978
Water1,02757
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)119,17618
Polymers115,9832
Non-polymers3,19416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5820 Å2
ΔGint-10 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.575, 86.621, 80.991
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 57991.320 Da / Num. of mol.: 1 / Mutation: R375A
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.: 57 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
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: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→47.31 Å / Num. obs: 35182 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.99 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 3497 / CC1/2: 0.712

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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: 2.1→43.576 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1653 4.7 %
Rwork0.1795 33528 -
obs0.1806 35181 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.51 Å2 / Biso mean: 52.6282 Å2 / Biso min: 28.53 Å2
Refinement stepCycle: final / Resolution: 2.1→43.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 108 57 4170
Biso mean--91.48 53.54 -
Num. residues----505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.16180.27161430.26822752
2.1618-2.23160.28641220.24412830
2.2316-2.31130.25451150.22942777
2.3113-2.40390.24431390.20162788
2.4039-2.51330.20451460.18452755
2.5133-2.64580.21560.17182789
2.6458-2.81150.18311430.16292784
2.8115-3.02850.19541440.1672771
3.0285-3.33320.20061400.17862789
3.3332-3.81530.20581340.16562812
3.8153-4.80590.19241240.16332832
4.8059-43.5760.18531470.18352849
Refinement TLS params.Method: refined / Origin x: -17.3814 Å / Origin y: -13.9176 Å / Origin z: 21.5574 Å
111213212223313233
T0.3476 Å20.0187 Å20.0064 Å2-0.3313 Å20.0085 Å2--0.3312 Å2
L0.7623 °2-0.149 °20.1497 °2-0.7029 °20.122 °2--0.6976 °2
S-0.0681 Å °0.0596 Å °0.0156 Å °0.028 Å °0.0195 Å °0.0954 Å °-0.046 Å °-0.0334 Å °0 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 DIFFRACTION1allS1 - 57

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