+Open data
-Basic information
Entry | Database: PDB / ID: 6q4p | |||||||||
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Title | Fusidic acid bound AcrB_N298A | |||||||||
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 / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Tam, H.K. / Pos, K.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Binding and Transport of Carboxylated Drugs by the Multidrug Transporter AcrB. Authors: Tam, H.K. / Malviya, V.N. / Foong, W.E. / Herrmann, A. / Malloci, G. / Ruggerone, P. / Vargiu, A.V. / 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 | 6q4p.cif.gz | 685.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q4p.ent.gz | 551.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q4p_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6q4p_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6q4p_validation.xml.gz | 118.4 KB | Display | |
Data in CIF | 6q4p_validation.cif.gz | 162.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/6q4p ftp://data.pdbj.org/pub/pdb/validation_reports/q4/6q4p | HTTPS FTP |
-Related structure data
Related structure data | 6q4nC 6q4oC 5jmnS 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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-Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 114693.273 Da / Num. of mol.: 3 / Mutation: N298A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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 BL21(DE3) (bacteria) / Variant (production host): XL1 Blue |
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-Sugars , 1 types, 10 molecules
#3: Sugar | ChemComp-LMT / |
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-Non-polymers , 14 types, 556 molecules
#4: Chemical | #5: Chemical | ChemComp-DDQ / #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | ChemComp-FUA / | #9: Chemical | #10: Chemical | ChemComp-DDR / ( | #11: Chemical | #12: Chemical | ChemComp-CL / #13: Chemical | #14: Chemical | ChemComp-D10 / | #15: Chemical | ChemComp-C14 / | #16: Chemical | ChemComp-ETE / | #17: 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: 3.7 Å3/Da / Density % sol: 66.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.05M ADA, pH 6.6, 0.15-0.25M AMMONIUM SULFATE, 5% GLYCEROL, 8-9% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.76 Å / Num. obs: 144226 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 1.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JMN Resolution: 2.8→49.76 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 14.691 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.595 / ESU R Free: 0.313 / 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: 58.741 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→49.76 Å
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