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Yorodumi- PDB-5h36: Crystal structures of the TRIC trimeric intracellular cation chan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h36 | ||||||
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Title | Crystal structures of the TRIC trimeric intracellular cation channel orthologue from Rhodobacter sphaeroides | ||||||
Components | Uncharacterized protein TRIC | ||||||
Keywords | MEMBRANE PROTEIN / ion channels | ||||||
Function / homology | Glycine transporter / Glycine transporter / membrane => GO:0016020 / plasma membrane / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Uncharacterized protein Function and homology information | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.409 Å | ||||||
Authors | Kasuya, G. / Hiraizumi, M. / Hattori, M. / Nureki, O. | ||||||
Citation | Journal: Cell Res. / Year: 2016 Title: Crystal structures of the TRIC trimeric intracellular cation channel orthologues Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / ...Authors: Kasuya, G. / Hiraizumi, M. / Maturana, A.D. / Kumazaki, K. / Fujiwara, Y. / Liu, K. / Nakada-Nakura, Y. / Iwata, S. / Tsukada, K. / Komori, T. / Uemura, S. / Goto, Y. / Nakane, T. / Takemoto, M. / Kato, H.E. / Yamashita, K. / Wada, M. / Ito, K. / Ishitani, R. / Hattori, M. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h36.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h36.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h36_validation.pdf.gz | 724.5 KB | Display | wwPDB validaton report |
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Full document | 5h36_full_validation.pdf.gz | 731.9 KB | Display | |
Data in XML | 5h36_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5h36_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/5h36 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/5h36 | HTTPS FTP |
-Related 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
#1: Protein | Mass: 22783.598 Da / Num. of mol.: 2 / Fragment: UNP residues 1-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria) Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_3856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HKN0 #2: Chemical | |
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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: 4.23 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 25-32% (v/v) PEG 400, 20-70mM Li2SO4, 20-70mM Na2SO4, 50mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.409→50 Å / Num. obs: 9730 / % possible obs: 95.3 % / Redundancy: 5.1 % / Net I/σ(I): 15.2 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 3.409→45.036 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.409→45.036 Å
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Refine LS restraints |
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LS refinement shell |
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