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Yorodumi- PDB-5lj6: Structure of Aggregatibacter actinomycetemcomitans MacB bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lj6 | ||||||
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Title | Structure of Aggregatibacter actinomycetemcomitans MacB bound to ATPyS (P6522) | ||||||
Components | Macrolide export ATP-binding/permease protein MacB | ||||||
Keywords | TRANSPORT PROTEIN / Membrane Protein ABC Transporter | ||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aggregatibacter actinomycetemcomitans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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 | 5lj6.cif.gz | 234.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lj6.ent.gz | 188.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/5lj6 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/5lj6 | HTTPS FTP |
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-Related structure data
Related structure data | 5lilC 5lj7C 5lj8C 5lj9C 5ljaC 5naaC 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
#1: Protein | Mass: 72114.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria) Gene: macB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 References: UniProt: Q2EHL8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.07 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: PEG 400, Sodium Citrate, Magnesium Chloride, ATPyS, Dodecylmaltopyranoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97943 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→61.56 Å / Num. obs: 21959 / % possible obs: 97.9 % / Redundancy: 13.8 % / Rsym value: 0.103 / Net I/σ(I): 10.3 |
Reflection shell | Highest resolution: 3.9 Å / Rsym value: 2.466 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Higher resolution MacB structure in space group P21 Resolution: 3.9→59.785 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 34.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→59.785 Å
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Refine LS restraints |
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LS refinement shell |
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