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Yorodumi- PDB-4zjq: Crystal structure of AcrB deletion mutant in complex with antibio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zjq | ||||||
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Title | Crystal structure of AcrB deletion mutant in complex with antibiotic in P21 space group | ||||||
Components | Multidrug efflux pump subunit AcrB | ||||||
Keywords | TRANSPORT 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.592 Å | ||||||
Authors | Ababou, A. / Koronakis, V. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Plos One / Year: 2016 Title: Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate. Authors: Ababou, A. / Koronakis, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zjq.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4zjq.ent.gz | 953.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zjq_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4zjq_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4zjq_validation.xml.gz | 247.2 KB | Display | |
Data in CIF | 4zjq_validation.cif.gz | 325.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zjq ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zjq | HTTPS FTP |
-Related structure data
Related structure data | 4zitC 4zivC 4ziwC 4zjlC 4zjoC 2gifS 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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Unit cell |
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-Components
#1: Protein | Mass: 113085.523 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: acrB, acrE, b0462, JW0451 / Production host: Escherichia coli (E. coli) / References: UniProt: P31224 #2: Chemical | #3: Sugar | ChemComp-LMT / #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.61 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 0.2 M MgAc, 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.59→125.83 Å / Num. obs: 114348 / % possible obs: 100 % / Redundancy: 6.1 % / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.59→3.79 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GIF Resolution: 3.592→19.963 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.592→19.963 Å
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Refine LS restraints |
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LS refinement shell |
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