+Open data
-Basic information
Entry | Database: PDB / ID: 6vs2 | ||||||
---|---|---|---|---|---|---|---|
Title | protein D | ||||||
Components | Multidrug transporter MdfA | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein | ||||||
Function / homology | Function and homology information potassium:proton antiporter activity / sodium:proton antiporter activity / xenobiotic detoxification by transmembrane export across the plasma membrane / regulation of cellular pH / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Lu, M. / Lu, M.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Structure and mechanism of a redesigned multidrug transporter from the Major Facilitator Superfamily. Authors: Wu, H.H. / Symersky, J. / Lu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vs2.cif.gz | 87 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vs2.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vs2_validation.pdf.gz | 475.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vs2_full_validation.pdf.gz | 485.8 KB | Display | |
Data in XML | 6vs2_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 6vs2_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/6vs2 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vs2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41923.020 Da / Num. of mol.: 1 / Mutation: E26T/D34M/A150E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mdfA, cmlA, cmr, b0842, JW0826 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY8 |
---|---|
#2: Chemical | ChemComp-LDA / |
#3: Chemical | ChemComp-PR / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.54 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG, salts, etc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. obs: 12518 / % possible obs: 99 % / Redundancy: 5 % / CC1/2: 1 / Rsym value: 0.06 / Net I/σ(I): 37 |
Reflection shell | Resolution: 3→3.1 Å / Num. unique obs: 300 / CC1/2: 0.4 / Rsym value: 0.6 / % possible all: 86 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 3→15 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||
Displacement parameters | Biso max: 357.8 Å2 / Biso mean: 169.4549 Å2 / Biso min: 62.21 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→15 Å
|