[English] 日本語
Yorodumi- PDB-5n6l: Structure of the membrane integral lipoprotein N-acyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n6l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the membrane integral lipoprotein N-acyltransferase Lnt C387A mutant from E. coli | ||||||
Components | Apolipoprotein N-acyltransferase | ||||||
Keywords | TRANSFERASE / membrane protein / lipoprotein / N-acyltransferase / lipidic cubic phase | ||||||
Function / homology | Function and homology information apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huang, C.-Y. / Boland, C. / Howe, N. / Wiktor, M. / Vogeley, L. / Weichert, D. / Bailey, J. / Olieric, V. / Wang, M. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis. Authors: Wiktor, M. / Weichert, D. / Howe, N. / Huang, C.Y. / Olieric, V. / Boland, C. / Bailey, J. / Vogeley, L. / Stansfeld, P.J. / Buddelmeijer, N. / Wang, M. / Caffrey, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5n6l.cif.gz | 221.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5n6l.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 5n6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/5n6l ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n6l | HTTPS FTP |
---|
-Related structure data
Related structure data | 5n6hSC 5n6mC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59248.695 Da / Num. of mol.: 2 / Mutation: C387A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Cell (production host): C43 / Production host: Escherichia coli (E. coli) References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 8 % (v/v) MPD 0.1 M MES pH 6 0.4 M ammonium citrate 0.1 M sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.79 Å / Num. obs: 34916 / % possible obs: 97.9 % / Redundancy: 5.4 % / Net I/σ(I): 7.72 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N6H Resolution: 2.9→49.79 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.36
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.79 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|