+Open data
-Basic information
Entry | Database: PDB / ID: 4pd5 | ||||||
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Title | Crystal structure of vcCNT-7C8C bound to gemcitabine | ||||||
Components | NupC family protein | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / gemcitabine / drug transporter | ||||||
Function / homology | Function and homology information nucleoside transmembrane transport / nucleoside transmembrane transporter activity / pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / symporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.906 Å | ||||||
Authors | Johnson, Z.L. / Lee, S.-Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2014 Title: Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters. Authors: Johnson, Z.L. / Lee, J.H. / Lee, K. / Lee, M. / Kwon, D.Y. / Hong, J. / 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 | 4pd5.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pd5.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/4pd5 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/4pd5 | HTTPS FTP |
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-Related structure data
Related structure data | 4pb1C 4pb2C 4pd6C 4pd7C 4pd8C 4pd9C 4pdaC 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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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 44151.848 Da / Num. of mol.: 1 / Mutation: L7C, I8C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_2352 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9KPL5 |
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#2: Chemical | ChemComp-GEO / |
#3: Chemical | ChemComp-NA / |
#4: Sugar | ChemComp-DMU / |
#5: 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: 4.01 Å3/Da / Density % sol: 69.29 % |
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Crystal grow | Temperature: 290 K / Method: liquid diffusion / pH: 8.5 / Details: 37-42% PEG400, 100 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0004 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 14694 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 82.67 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.059 / Net I/av σ(I): 30.765 / Net I/σ(I): 11.5 / Num. measured all: 83148 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TIJ Resolution: 2.906→43.684 Å / FOM work R set: 0.7644 / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.47 Å2 / Biso mean: 76.81 Å2 / Biso min: 38.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.906→43.684 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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