+Open data
-Basic information
Entry | Database: PDB / ID: 5wud | ||||||
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Title | Structural basis for conductance through TRIC cation channels | ||||||
Components | Uncharacterized protein | ||||||
Keywords | MEMBRANE PROTEIN / TRIC / cation channel / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS | ||||||
Function / homology | Glycine transporter / Glycine transporter / metal ion binding / plasma membrane / Glycine transporter domain-containing protein Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Su, M. / Gao, F. / Mao, Y. / Li, D.L. / Guo, Y.Z. / Wang, X.H. / Bruni, R. / Kloss, B. / Hendrickson, W.A. / Chen, Y.H. / New York Consortium on Membrane Protein Structure (NYCOMPS) | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis for conductance through TRIC cation channels. Authors: Su, M. / Gao, F. / Yuan, Q. / Mao, Y. / Li, D.L. / Guo, Y. / Yang, C. / Wang, X.H. / Bruni, R. / Kloss, B. / Zhao, H. / Zeng, Y. / Zhang, F.B. / Marks, A.R. / Hendrickson, W.A. / Chen, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wud.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wud.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wud_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 5wud_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 5wud_validation.xml.gz | 10 KB | Display | |
Data in CIF | 5wud_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wud ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wud | HTTPS FTP |
-Related structure data
Related structure data | 5wucSC 5wueC 5wufC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25716.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Gene: ATY89_00310, ATZ20_03355 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: A0A0U3H1E6 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.16 % |
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Crystal grow | Temperature: 291 K / Method: lipidic cubic phase / pH: 7 Details: PEG 200 38%, RbCl 100mM, MgCl2 100mM, HEPES pH 7.0 100mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.8153 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.8153 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.8→46.031 Å / Num. obs: 17832 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 22.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0246 / Net I/σ(I): 14.5 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WUC Resolution: 1.9→46.031 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||
Displacement parameters | Biso max: 74.66 Å2 / Biso mean: 24.4216 Å2 / Biso min: 12.41 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.031 Å
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