+Open data
-Basic information
Entry | Database: PDB / ID: 5lj8 | ||||||
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Title | Structure of the E. coli MacB periplasmic domain (P21) | ||||||
Components | Macrolide export ATP-binding/permease protein MacB | ||||||
Keywords | TRANSPORT PROTEIN / Membrane Protein ABC Transporter | ||||||
Function / homology | Function and homology information MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane ...MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Crow, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily. Authors: Crow, A. / Greene, N.P. / Kaplan, E. / Koronakis, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lj8.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lj8.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/5lj8 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/5lj8 | HTTPS FTP |
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-Related structure data
Related structure data | 5lilC 5lj6C 5lj7C 5lj9C 5ljaC 5naaC 3ftjS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 311 - 506 / Label seq-ID: 4 - 199
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-Components
#1: Protein | Mass: 23614.443 Da / Num. of mol.: 2 / Fragment: UNP residues 309-508 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: macB, ybjZ, b0879, JW0863 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: P75831, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #2: 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: 1.94 Å3/Da / Density % sol: 36.74 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 30% Pentaerythritol ethoxylate (15/4 EO/OH), 6% polyvinylpyrrolidone, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→66.81 Å / Num. obs: 25260 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 8.1 |
Reflection shell | Rsym value: 0.542 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ftj Resolution: 1.95→32.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.376 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.165 / 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: 25.77 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→32.87 Å
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Refine LS restraints |
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