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- PDB-5ofr: Structure of the antibacterial peptide ABC transporter McjD in a ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ofr | ||||||
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Title | Structure of the antibacterial peptide ABC transporter McjD in a high energy outward occluded intermediate state | ||||||
![]() | Microcin-J25 export ATP-binding/permease protein McjD | ||||||
![]() | MEMBRANE PROTEIN / ABC transporter / antibacterial peptide / high energy outward occluded intermediate / ADP-VO4 | ||||||
Function / homology | ![]() bacteriocin transport / bacteriocin immunity / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / protein transport / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beis, K. / Bountra, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD. Authors: Bountra, K. / Hagelueken, G. / Choudhury, H.G. / Corradi, V. / El Omari, K. / Wagner, A. / Mathavan, I. / Zirah, S. / Yuan Wahlgren, W. / Tieleman, D.P. / Schiemann, O. / Rebuffat, S. / Beis, K. #1: ![]() Title: Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state. Authors: Choudhury, H.G. / Tong, Z. / Mathavan, I. / Li, Y. / Iwata, S. / Zirah, S. / Rebuffat, S. / van Veen, H.W. / Beis, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.8 KB | Display | ![]() |
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PDB format | ![]() | 190.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ofpC ![]() 4pl0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 65482.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9X2W0 #2: Chemical | #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.33 Å3/Da / Density % sol: 76.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 10% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol |
-Data collection
Diffraction | Mean temperature: 60 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.26 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→95.3 Å / Num. obs: 22352 / % possible obs: 94.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 98.36 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 3.4→3.46 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 437 / CC1/2: 0.86 / % possible all: 87.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4pl0 Resolution: 3.4→95.3 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.835 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.647
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Displacement parameters | Biso mean: 108.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.4→95.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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