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Yorodumi- PDB-5n6m: Structure of the membrane integral lipoprotein N-acyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n6m | ||||||
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Title | Structure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa | ||||||
Components | Apolipoprotein N-acyltransferase | ||||||
Keywords | MEMBRANE PROTEIN / lipoprotein / N-acyltransferase / lipidic cubic phase | ||||||
Function / homology | Function and homology information apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n6m.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n6m.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 5n6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n6m_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5n6m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5n6m_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 5n6m_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/5n6m ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n6m | HTTPS FTP |
-Related structure data
Related structure data | 5n6hSC 5n6lC S: Starting model for refinement 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: 58230.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lnt, cutE, PA3984 / Cell line (production host): C41 / Production host: Pseudomonas aeruginosa (bacteria) References: UniProt: Q9ZI86, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FLC / | #4: Chemical | ChemComp-OLC / ( #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100 mM NaCitrate pH 5.0 30 % (v/v) PEG-500 DME 100 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0003 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0003 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.5 Å / Num. obs: 10159 / % possible obs: 98.9 % / Redundancy: 5.4 % / Net I/σ(I): 6.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N6H Resolution: 3.1→49.5 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→49.5 Å
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Refine LS restraints |
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LS refinement shell |
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