+Open data
-Basic information
Entry | Database: PDB / ID: 5naa | ||||||
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Title | Lipoprotein-releasing system transmembrane protein LolC | ||||||
Components | Lipoprotein-releasing system transmembrane protein LolC | ||||||
Keywords | PROTEIN TRANSPORT / Periplasmic domain | ||||||
Function / homology | Function and homology information lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / lipoprotein transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Kaplan, E. | ||||||
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 | 5naa.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5naa.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 5naa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/5naa ftp://data.pdbj.org/pub/pdb/validation_reports/na/5naa | HTTPS FTP |
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-Related structure data
Related structure data | 5lilSC 5lj6C 5lj7C 5lj8C 5lj9C 5ljaC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 48 - 264 / Label seq-ID: 1 - 217
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-Components
#1: Protein | Mass: 25623.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADC3 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6, 30% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→45.99 Å / Num. obs: 34822 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.88→1.92 Å / Rmerge(I) obs: 0.436 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LIL Resolution: 1.88→45.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.718 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.454 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→45.99 Å
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Refine LS restraints |
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