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Yorodumi- PDB-6lgv: Crystal structure of a cysteine-pair mutant (P10C-S291C) of a bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lgv | ||||||
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Title | Crystal structure of a cysteine-pair mutant (P10C-S291C) of a bacterial bile acid transporter in an inward-facing state complexed with citrate | ||||||
Components | Transporter, sodium/bile acid symporter family | ||||||
Keywords | TRANSPORT PROTEIN / Bile acid transporter / ASBT / NTCP / SLC10 | ||||||
Function / homology | bile acid:sodium symporter activity / 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: 1.847 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: Substrate binding in the bile acid transporter ASBT Yf from Yersinia frederiksenii. 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 | 6lgv.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lgv.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lgv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6lgv_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6lgv_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 6lgv_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lgv ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lgv | HTTPS FTP |
-Related structure data
Related structure data | 6lgyC 6lgzC 6lh0C 4n7wS 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: 33387.898 Da / Num. of mol.: 1 / Mutation: P10C, S291C 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 | ChemComp-A6L / #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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 4.5 Details: 0.1 M NaCl, 0.1 M MgCl2, 0.1 M Na+-citrate pH 4.5, 32% (v/v) PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.847→40.3 Å / Num. obs: 24982 / % possible obs: 95.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.044 / Rrim(I) all: 0.112 / Net I/σ(I): 12.1 / Num. measured all: 156974 | ||||||||||||||||||||||||||||||
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: 4N7W Resolution: 1.847→40.3 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.49 / 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: 90.56 Å2 / Biso mean: 27.129 Å2 / Biso min: 10.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.847→40.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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