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Yorodumi- PDB-6nwr: Thioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nwr | ||||||
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Title | Thioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt) | ||||||
Components | (Apolipoprotein N-acyltransferase) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / Enzyme / Nitrilase / N-acyltransferase / Lipoprotein | ||||||
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 / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Wiseman, B. / Hogbom, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Conformational changes in Apolipoprotein N-acyltransferase (Lnt). Authors: Wiseman, B. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nwr.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nwr.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nwr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6nwr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6nwr_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 6nwr_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nwr ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nwr | HTTPS FTP |
-Related structure data
Related structure data | 6q3aC 5n6lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58988.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): C41 References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
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#2: Protein | Mass: 59226.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): C41 References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
#3: Sugar | #4: Chemical | ChemComp-D12 / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.42 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 25 % PEG 2000MME, 100 mM Na cacodylate, 40 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.5→48.47 Å / Num. obs: 28448 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.277 / Net I/σ(I): 5.1 | |||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N6L Resolution: 3.5→48.469 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.04 Å2 / Biso mean: 109.6441 Å2 / Biso min: 36.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→48.469 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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