+Open data
-Basic information
Entry | Database: PDB / ID: 5jmn | |||||||||
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Title | Fusidic acid bound AcrB | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Multidrug efflux protein / Membrane protein | |||||||||
Function / homology | Function and homology information xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Oswald, C. / Tam, H.K. / Pos, K.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2016 Title: Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB. Authors: Oswald, C. / Tam, H.K. / Pos, K.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jmn.cif.gz | 694.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jmn.ent.gz | 559.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jmn_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 5jmn_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 5jmn_validation.xml.gz | 122.1 KB | Display | |
Data in CIF | 5jmn_validation.cif.gz | 170.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/5jmn ftp://data.pdbj.org/pub/pdb/validation_reports/jm/5jmn | HTTPS FTP |
-Related structure data
Related structure data | 4dx7S 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
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 114736.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P31224 #2: Protein | Mass: 18317.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: Artificial gene / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue |
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-Sugars , 1 types, 10 molecules
#4: Sugar | ChemComp-LMT / |
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-Non-polymers , 11 types, 846 molecules
#3: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PTY / #10: Chemical | ChemComp-D12 / #11: Chemical | #12: Chemical | ChemComp-P3G / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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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: 3.84 Å3/Da / Density % sol: 67.97 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.05M ADA, pH 6.9, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 5-10% PEG4000, 0.004m FUSIDIC ACID |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.15 Å / Num. obs: 259156 / % possible obs: 92.8 % / Redundancy: 6.7 % / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DX7 Resolution: 2.5→49.15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.8 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.517 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→49.15 Å
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Refine LS restraints |
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