[English] 日本語
Yorodumi- PDB-4zp0: Crystal structure of E. coli multidrug transporter MdfA in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zp0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli multidrug transporter MdfA in complex with deoxycholate | ||||||
Components | Multidrug transporter MdfA | ||||||
Keywords | TRANSPORT PROTEIN / MFS family / Multi-drug antiporter / MDFA / Cm | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhang, X.C. / Heng, J. / Zhao, Y. / Wang, X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Cell Res. / Year: 2015 Title: Substrate-bound structure of the E. coli multidrug resistance transporter MdfA Authors: Heng, J. / Zhao, Y. / Liu, M. / Liu, Y. / Fan, J. / Wang, X. / Zhao, Y. / Zhang, X.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zp0.cif.gz | 90 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zp0.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zp0_validation.pdf.gz | 735 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4zp0_full_validation.pdf.gz | 744.7 KB | Display | |
Data in XML | 4zp0_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4zp0_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/4zp0 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/4zp0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42461.629 Da / Num. of mol.: 1 / Fragment: UNP residues 9-400 / Mutation: Q123R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: mdfA, cmlA, cmr, b0842, JW0826 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0AEY8 | ||
---|---|---|---|
#2: Chemical | ChemComp-DXC / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.92 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 400, 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 11.7 % / Number: 135599 / Rmerge(I) obs: 0.142 / Χ2: 1.03 / D res high: 3 Å / D res low: 50 Å / Num. obs: 11581 / % possible obs: 99.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 38240 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.62 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.067 / Net I/av σ(I): 12.133 / Net I/σ(I): 9.6 / Num. measured all: 131212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.466 Å / FOM work R set: 0.8195 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.33 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.11 Å2 / Biso mean: 58.49 Å2 / Biso min: 38.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→44.466 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|