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- PDB-6yu6: Crystal structure of MhsT in complex with L-leucine -

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Basic information

Entry
Database: PDB / ID: 6yu6
TitleCrystal structure of MhsT in complex with L-leucine
ComponentsSodium-dependent transporter
KeywordsTRANSPORT PROTEIN / LeuT-fold / amino acid transporter / L-leucine
Function / homology: / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / membrane / LEUCINE / Na+-dependent transporter / Sodium-dependent transporter
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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

Downloads & links

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Assembly

Deposited unit
A: Sodium-dependent transporter
B: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35216
Polymers96,7222
Non-polymers3,63114
Water82946
1
A: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6879
Polymers48,3611
Non-polymers2,3268
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6657
Polymers48,3611
Non-polymers1,3056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.230, 215.560, 50.170
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 8 molecules

#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Sugar
ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 3 types, 52 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.26 %
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, 0.1M 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: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.35→45.5 Å / Num. obs: 38291 / % possible obs: 98.5 % / Redundancy: 3 % / CC1/2: 0.996 / Net I/σ(I): 8.1
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 3843 / CC1/2: 0.511

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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: 2.35→45.484 Å / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 23.51
RfactorNum. reflection% reflection
Rfree0.2222 1943 5.07 %
Rwork0.1852 --
obs0.1919 38291 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 41.5976 Å2 / Biso min: 28.21 Å2
Refinement stepCycle: final / Resolution: 2.35→45.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6678 0 198 46 6922
Biso mean--49.75 37.89 -
Num. residues----887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3676-2.42550.30372000.262414261491
2.4255-2.48950.3165970.26072546264395
2.4895-2.56090.2781950.25962488258395
2.5609-2.64120.26541930.24822428262191
2.6412-2.73270.2861970.23812482257994
2.7327-2.83830.2886950.2282498259394
2.8383-2.96240.27781940.22152454264890
2.9624-3.11160.2479960.20572470256695
3.1116-3.29610.21671940.19442410260491
3.2961-3.53410.2098980.18192554265296
3.5341-3.86010.2456960.16452534263096
3.8601-4.35380.19511900.16542440263092
4.3538-5.26620.2021950.15242552264795
5.2662-8.590.19441780.16952460263892

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