+Open data
-Basic information
Entry | Database: PDB / ID: 5l2b | ||||||
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Title | Structure of CNTnw N149S, E332A in an outward-facing state | ||||||
Components | Nucleoside permease | ||||||
Keywords | TRANSPORT PROTEIN / transporter / nucleoside / elevator-type alternate access | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neisseria wadsworthii 9715 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 | 5l2b.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l2b.ent.gz | 182.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l2b ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l2b | HTTPS FTP |
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-Related structure data
Related structure data | 5l24C 5l26SC 5l27C 5l2aC 5u9wC 5l28 5l29 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44589.488 Da / Num. of mol.: 3 / Mutation: N149S, E322A 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) / Strain (production host): C41 / References: UniProt: G4CRQ5 #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: 4.39 Å3/Da / Density % sol: 71.96 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM choline chloride, 14% Poly(ethylene glycol) monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→98.06 Å / Num. obs: 22489 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.8→4.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / CC1/2: 0.54 / Rpim(I) all: 0.54 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L26 Resolution: 3.8→98.058 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.37 / 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: 3.8→98.058 Å
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Refine LS restraints |
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LS refinement shell |
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