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- PDB-6yu2: Crystal structure of MhsT in complex with L-isoleucine -

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Basic information

Entry
Database: PDB / ID: 6yu2
TitleCrystal structure of MhsT in complex with L-isoleucine
ComponentsSodium-dependent transporter
KeywordsTRANSPORT PROTEIN / LeuT-fold / amino acid transporter / L-isoleucine
Function / homology: / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / membrane / ISOLEUCINE / Na+-dependent transporter / Sodium-dependent transporter
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsFocht, D. / Neumann, C. / Lyons, J. / Eguskiza Bilbao, A. / Blunck, R. / Malinauskaite, L. / Schwarz, I.O. / Javitch, J.A. / Quick, M. / Nissen, P.
Funding support Denmark, 4items
OrganizationGrant numberCountry
Lundbeckfonden2011-3868 Denmark
Lundbeckfonden2015-2704 Denmark
Lundbeckfonden2015-3225 Denmark
Lundbeckfonden2016-2518 Denmark
CitationJournal: Embo J. / Year: 2021
Title: A non-helical region in transmembrane helix 6 of hydrophobic amino acid transporter MhsT mediates substrate recognition.
Authors: Focht, D. / Neumann, C. / Lyons, J. / Eguskiza Bilbao, A. / Blunck, R. / Malinauskaite, L. / Schwarz, I.O. / Javitch, J.A. / Quick, M. / Nissen, P.
History
DepositionApr 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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: Sodium-dependent transporter
B: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,83014
Polymers96,7222
Non-polymers2,10912
Water30617
1
A: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4157
Polymers48,3611
Non-polymers1,0546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4157
Polymers48,3611
Non-polymers1,0546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.950, 97.290, 110.940
Angle α, β, γ (deg.)90.000, 96.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sodium-dependent transporter


Mass: 48360.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: E2L07_01100 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A4Y7X244, UniProt: Q9KDT3*PLUS
#2: 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ILE / ISOLEUCINE / Isoleucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystallized using HiLiDe with DOPC as added lipid. Crystals were obtained in 14-24% PEG400, 0.3-0.5M NaCl, 0.1 M Tris-HCl or HEPES-NaOH pH 7.0, 5% Trimethylamine N-oxide (TMANO), 5% or 10% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.1→43.7 Å / Num. obs: 13856 / % possible obs: 81.6 % / Redundancy: 2.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.195 / Net I/σ(I): 3.6
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 2557 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4US3

4us3


Resolution: 3.1→43.698 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.51
RfactorNum. reflection% reflection
Rfree0.305 674 4.88 %
Rwork0.2769 --
obs0.2783 13817 81.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.23 Å2 / Biso mean: 56.685 Å2 / Biso min: 43.64 Å2
Refinement stepCycle: final / Resolution: 3.1→43.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6630 0 131 17 6778
Biso mean--57.22 52.18 -
Num. residues----882
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1003-3.33960.35481360.3398270784
3.3396-3.67550.36321360.3102269484
3.6755-4.2070.30871350.2686261582
4.207-5.29890.26071350.2577259580
5.2989-43.690.29721320.2588253277

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