[English] 日本語
Yorodumi- PDB-6xgy: Crystal structure of E. coli MlaFB ABC transport subunits in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xgy | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli MlaFB ABC transport subunits in the dimeric state | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | LIPID TRANSPORT / ABC transporters / MlaF / MlaB / bacterial outer membrane / ATPase / regulation / STAS domain | ||||||||||||||||||
Function / homology | Function and homology information phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid-translocating ATPase complex / phospholipid transport / ATPase-coupled transmembrane transporter activity / response to antibiotic / DNA damage response / ATP binding / membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli LAU-EC10 (bacteria) Escherichia coli (E. coli) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Chang, Y. / Bhabha, G. / Ekiert, D.C. | ||||||||||||||||||
Funding support | United States, 5items
| ||||||||||||||||||
Citation | Journal: Elife / Year: 2020 Title: Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation. Authors: Kolich, L.R. / Chang, Y.T. / Coudray, N. / Giacometti, S.I. / MacRae, M.R. / Isom, G.L. / Teran, E.M. / Bhabha, G. / Ekiert, D.C. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xgy.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xgy.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 6xgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/6xgy ftp://data.pdbj.org/pub/pdb/validation_reports/xg/6xgy | HTTPS FTP |
---|
-Related structure data
Related structure data | 6xgzC 2oukS 3f43S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29128.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli LAU-EC10 (bacteria) / Gene: V415_03760 / Plasmid: pBEL1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: V8KL36 | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 12314.044 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mlaB, yrbB / Plasmid: pBEL1307 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: W8T4U6, UniProt: P64602*PLUS | ||||
#3: Chemical | ChemComp-ADP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.68 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2016 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→44.57 Å / Num. obs: 12466 / % possible obs: 93.09 % / Redundancy: 19.7 % / CC1/2: 0.999 / Net I/σ(I): 16.09 |
Reflection shell | Resolution: 2.9→3.004 Å / Num. unique obs: 1213 / CC1/2: 0.349 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUK, 3F43 Resolution: 2.9→44.57 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.37 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 181.18 Å2 / Biso mean: 84.1482 Å2 / Biso min: 36.55 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→44.57 Å
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -35.9284 Å / Origin y: 17.9383 Å / Origin z: 3.3316 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|