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Open data
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Basic information
Entry | Database: PDB / ID: 5lj8 | ||||||
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Title | Structure of the E. coli MacB periplasmic domain (P21) | ||||||
![]() | Macrolide export ATP-binding/permease protein MacB | ||||||
![]() | TRANSPORT PROTEIN / Membrane Protein ABC Transporter | ||||||
Function / homology | ![]() MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding ...MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter activity / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crow, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.5 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 441.4 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lilC ![]() 5lj6C ![]() 5lj7C ![]() 5lj9C ![]() 5ljaC ![]() 5naaC ![]() 3ftjS 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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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: _ / 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: _ / 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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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