+Open data
-Basic information
Entry | Database: PDB / ID: 6yu5 | |||||||||||||||
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Title | Crystal structure of MhsT in complex with L-valine | |||||||||||||||
Components | Sodium-dependent transporter | |||||||||||||||
Keywords | TRANSPORT PROTEIN / LeuT-fold / amino acid transporter / L-valine | |||||||||||||||
Function / homology | : / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / membrane / VALINE / Na+-dependent transporter / Sodium-dependent transporter Function and homology information | |||||||||||||||
Biological species | Bacillus halodurans (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 6yu5.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yu5.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 6yu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yu5_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 6yu5_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 6yu5_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 6yu5_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yu5 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yu5 | HTTPS FTP |
-Related structure data
Related structure data | 6yu2C 6yu3C 6yu4C 6yu6C 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, 22 molecules
#4: Sugar | ChemComp-BNG / #5: Sugar | |
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-Non-polymers , 3 types, 79 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #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: 2.48 Å3/Da / Density % sol: 50.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop 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: I24 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.1 Å / Num. obs: 28702 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.994 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.6→2.72 Å / Num. unique obs: 2849 / CC1/2: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4US3 Resolution: 2.6→49.045 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.54 Å2 / Biso mean: 57.4168 Å2 / Biso min: 41.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→49.045 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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