+Open data
-Basic information
Entry | Database: PDB / ID: 3wdo | ||||||
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Title | Structure of E. coli YajR transporter | ||||||
Components | MFS Transporter | ||||||
Keywords | TRANSPORT PROTEIN / Motif A / Membrane potential / protonation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å | ||||||
Authors | Jiang, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A Authors: Jiang, D. / Zhao, Y. / Wang, X. / Fan, J. / Heng, J. / Liu, X. / Feng, W. / Kang, X. / Huang, B. / Liu, J. / Zhang, X.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdo.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdo.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdo ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48678.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21List of strains of Escherichia coli / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A140NCX4*PLUS |
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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: 4.06 Å3/Da / Density % sol: 69.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 5 Details: 30% PEG300, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.15→50 Å / Num. all: 14541 / Num. obs: 14541 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||||||||
Reflection shell | Resolution: 3.15→50 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.15→39.168 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7015 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 34.2 / Stereochemistry target values: MLHL
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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: 296.71 Å2 / Biso mean: 65.7669 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→39.168 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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