+Open data
-Basic information
Entry | Database: PDB / ID: 6yu6 | |||||||||||||||
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Title | Crystal structure of MhsT in complex with L-leucine | |||||||||||||||
Components | Sodium-dependent transporter | |||||||||||||||
Keywords | TRANSPORT 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 species | Bacillus halodurans (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||||||||
Authors | Focht, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yu6.cif.gz | 183.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yu6.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yu6 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yu6 | HTTPS FTP |
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-Related structure data
Related structure data | 6yu2C 6yu3C 6yu4C 6yu5C 6yu7C 4us3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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 / #5: Sugar | ChemComp-SOG / |
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-Non-polymers , 3 types, 52 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.48 |
Reflection | Resolution: 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 shell | Resolution: 2.35→2.43 Å / Num. unique obs: 3843 / CC1/2: 0.511 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4US3 Resolution: 2.35→45.484 Å / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 23.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.19 Å2 / Biso mean: 41.5976 Å2 / Biso min: 28.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→45.484 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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