[English] 日本語
Yorodumi- PDB-5lj7: Structure of Aggregatibacter actinomycetemcomitans MacB bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lj7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Aggregatibacter actinomycetemcomitans MacB bound to ATP (P21) | ||||||
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: 3.25 Å | ||||||
Authors | Crow, A. | ||||||
Funding support | United Kingdom, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lj7.cif.gz | 443.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lj7.ent.gz | 364.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/5lj7 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/5lj7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5lilSC 5lj6C 5lj8C 5lj9C 5ljaC 5naaC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 72114.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria) Gene: macB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: Q2EHL8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.93 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→86.13 Å / Num. obs: 70100 / % possible obs: 99.4 % / Redundancy: 6.1 % / Rsym value: 0.21 / Net I/σ(I): 6.7 |
Reflection shell | Highest resolution: 3.25 Å / Rsym value: 1.317 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LIL Resolution: 3.25→86.126 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 36.35
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→86.126 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|