+Open data
-Basic information
Entry | Database: PDB / ID: 5wuf | ||||||
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Title | Structural basis for conductance through TRIC cation channels | ||||||
Components | Putative membrane 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 / plasma membrane / : / Putative membrane protein Function and homology information | ||||||
Biological species | Colwellia psychrerythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.401 Å | ||||||
Authors | Mao, Y. / Gao, F. / Su, M. / Wang, X.H. / Zeng, Y. / 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 | 5wuf.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wuf.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wuf_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 5wuf_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 5wuf_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 5wuf_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/5wuf ftp://data.pdbj.org/pub/pdb/validation_reports/wu/5wuf | HTTPS FTP |
-Related structure data
Related structure data | 5wucC 5wudC 5wueC 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: 27795.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_4741 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q47UY7 | ||
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#2: Chemical | ChemComp-CD / #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: 3.65 Å3/Da / Density % sol: 66.29 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG400 38%, NaCl 100mM, CdCl2 100mM, Tris-HCl, pH 8.5, 100mM |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97876 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 28, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97876 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→45.66 Å / Num. obs: 30649 / % possible obs: 99.8 % / Redundancy: 73.6 % / Biso Wilson estimate: 61.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.197 / Net I/σ(I): 20.8 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.401→37.736 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.62 / Stereochemistry target values: ML Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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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: 213.45 Å2 / Biso mean: 74.0891 Å2 / Biso min: 37.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.401→37.736 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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