+Open data
-Basic information
Entry | Database: PDB / ID: 5l26 | ||||||
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Title | Structure of CNTnw in an inward-facing substrate-bound state | ||||||
Components | Nucleoside permease | ||||||
Keywords | TRANSPORT PROTEIN / transporter / nucleoside / elevator-type alternate access | ||||||
Function / homology | Function and homology information pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / plasma membrane Similarity search - Function | ||||||
Biological species | Neisseria wadsworthii 9715 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Hirschi, M. / Johnson, Z.L. / Lee, S.-Y. | ||||||
Citation | Journal: Nature / Year: 2017 Title: Visualizing multistep elevator-like transitions of a nucleoside transporter. Authors: Hirschi, M. / Johnson, Z.L. / Lee, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l26.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l26.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 5l26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l26 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l26 | HTTPS FTP |
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-Related structure data
Related structure data | 5l24C 5l27C 5l2aC 5l2bC 5u9wC 3tijS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44674.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria wadsworthii 9715 (bacteria) / Gene: nupC, HMPREF9370_1765 / Production host: Escherichia coli (E. coli) / References: UniProt: G4CRQ5 #2: Chemical | ChemComp-6ZL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 3.93 Å3/Da / Density % sol: 68.73 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1 M NaCl, 35% PEG400, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→55.052 Å / Num. obs: 53753 / % possible obs: 99.66 % / Redundancy: 7 % / CC1/2: 1 / Rpim(I) all: 0.08 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.4→3.61 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.48 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TIJ Resolution: 3.4→55.052 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 29.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→55.052 Å
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Refine LS restraints |
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LS refinement shell |
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