+Open data
-Basic information
Entry | Database: PDB / ID: 8k1r | ||||||||||||
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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: 2.6 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.S. / 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 | 8k1r.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k1r.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 8k1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k1r_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 8k1r_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 8k1r_validation.xml.gz | 34 KB | Display | |
Data in CIF | 8k1r_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/8k1r ftp://data.pdbj.org/pub/pdb/validation_reports/k1/8k1r | HTTPS FTP |
-Related structure data
Related structure data | 8j4cC 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: 49435.566 Da / Num. of mol.: 2 / Mutation: C22A,L415A 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 | ChemComp-OLC / ( #3: Water | ChemComp-HOH / | 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: 3.47 Å3/Da / Density % sol: 64.51 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.35 M Ammonium formate, 0.1M Tris-HCl pH 8.0-9.0, 26-36% 1,4- Butandiol |
-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: Jun 8, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.93 Å / Num. obs: 42977 / % possible obs: 99.52 % / Redundancy: 321.2 % / Biso Wilson estimate: 31.95 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.9879 / Rpim(I) all: 0.0478 / Rrim(I) all: 0.9893 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 2.6→2.693 Å / Redundancy: 297.1 % / Rmerge(I) obs: 5.227 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4206 / CC1/2: 0.861 / CC star: 0.962 / Rpim(I) all: 0.2706 / Rrim(I) all: 5.236 / % possible all: 99.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.93 Å / SU ML: 0.2607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7425 / Stereochemistry target values: GeoStd + Monomer Library
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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: 39.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.93 Å
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Refine LS restraints |
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LS refinement shell |
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