+Open data
-Basic information
Entry | Database: PDB / ID: 8j4c | ||||||||||||
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Title | YeeE(TsuA)-YeeD(TsuB) complex for thiosulfate uptake | ||||||||||||
Components | Spirochaeta thermophila YeeE(TsuA)-YeeD(TsuB),UPF0033 domain-containing protein, SirA-like domain-containing protein (chimera) | ||||||||||||
Keywords | TRANSPORT PROTEIN / Thiosulfate / Bacterial sulfur assimilation / membrane protein | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Spirochaeta thermophila DSM 6578 (bacteria) Corynebacterium pollutisoli (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å | ||||||||||||
Authors | Ikei, M. / Miyazaki, R. / Monden, K. / Naito, Y. / Takeuchi, A. / Takahashi, Y.S. / Tanaka, Y. / Ichikawa, M. / Tsukazaki, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: Structure and function of YeeE-YeeD complex for sophisticated thiosulfate uptake Authors: Ikei, M. / Miyazaki, R. / Monden, K. / Naito, Y. / Takeuchi, A. / Takahashi, Y. / Tanaka, Y. / Ichikawa, M. / Tsukazaki, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j4c.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j4c.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 8j4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/8j4c ftp://data.pdbj.org/pub/pdb/validation_reports/j4/8j4c | HTTPS FTP |
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-Related structure data
Related structure data | 8k1rC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49477.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spirochaeta thermophila DSM 6578 (bacteria), (gene. exp.) Corynebacterium pollutisoli (bacteria) Strain: DSM 6578 / Gene: Spith_0734, SAMN06295981_0228, Spith_0735 / Production host: Escherichia coli (E. coli) References: UniProt: G0GAP6, UniProt: A0A1X7HYM8, UniProt: G0GAP7 #2: Chemical | #3: Chemical | ChemComp-OLC / ( 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: 3.57 Å3/Da / Density % sol: 65.57 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 18-24% Pentaerythritol-propoxylate (5/4 PO/OH), 100 mM 2-morpholinoethanesulfonic acid (MES)-NaOH (pH 7.0), 300 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.34→49.39 Å / Num. obs: 21071 / % possible obs: 99.07 % / Redundancy: 20.4 % / Biso Wilson estimate: 49.19 Å2 / CC1/2: 0.964 / CC star: 0.991 / Rpim(I) all: 0.2815 / Rrim(I) all: 1.095 / Net I/σ(I): 4.15 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 18.5 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1989 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 1.012 / Rrim(I) all: 4.632 / % possible all: 97.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→49.39 Å / SU ML: 0.5452 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1098 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.34→49.39 Å
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Refine LS restraints |
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LS refinement shell |
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