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Yorodumi- PDB-6lh1: Crystal structure of a cysteine-pair mutant (Y113C-P190C) of a ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lh1 | ||||||
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Title | Crystal structure of a cysteine-pair mutant (Y113C-P190C) of a bacterial bile acid transporter trapped in an outward-facing conformation | ||||||
Components | Transporter, sodium/bile acid symporter familyTransport protein | ||||||
Keywords | TRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10 | ||||||
Function / homology | Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / CITRIC ACID / Transporter, sodium/bile acid symporter family Function and homology information | ||||||
Biological species | Yersinia frederiksenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.861 Å | ||||||
Authors | Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter. Authors: Wang, X. / Lyu, Y. / Ji, Y. / Sun, Z. / Zhou, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lh1.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lh1.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/6lh1 ftp://data.pdbj.org/pub/pdb/validation_reports/lh/6lh1 | HTTPS FTP |
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-Related structure data
Related structure data | 7cygC 7cykC 4n7xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33311.801 Da / Num. of mol.: 1 / Mutation: Y113C, P190C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia frederiksenii (bacteria) / Gene: NCTC11470_02445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A380PV03 | ||||
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#2: Chemical | ChemComp-CIT / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 5 Details: 0.2 M NH4H2PO4, 0.1 M (NH4)2SO4, 0.1 M Na+-citrate pH 5.0, 34% PEG 400, 4% 1,3-Butanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.851→48.279 Å / Num. obs: 7621 / % possible obs: 96.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 47.59 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.087 / Rrim(I) all: 0.171 / Net I/σ(I): 7.6 / Num. measured all: 27463 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7X Resolution: 2.861→48.279 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 89.3 Å2 / Biso mean: 42.6438 Å2 / Biso min: 19.08 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.861→48.279 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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