+Open data
-Basic information
Entry | Database: PDB / ID: 5w8s | ||||||||||||
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Title | Lipid A Disaccharide Synthase (LpxB)-7 solubilizing mutations | ||||||||||||
Components | Lipid-A-disaccharide synthase | ||||||||||||
Keywords | TRANSFERASE / glycosyltransferase B / Rossmann-like / C-terminal swap / dimer / lipid A disaccharide synthase / Raetz pathway / lipid A synthesis pathway / lipiopolysaccharide synthesis | ||||||||||||
Function / homology | Function and homology information lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / extrinsic component of cytoplasmic side of plasma membrane / phospholipid binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||||||||
Authors | Bohl, T.E. / Aihara, H. / Shi, K. / Lee, J.K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2018 Title: Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli. Authors: Bohl, T.E. / Shi, K. / Lee, J.K. / Aihara, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w8s.cif.gz | 222.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w8s.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w8s_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 5w8s_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 5w8s_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5w8s_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/5w8s ftp://data.pdbj.org/pub/pdb/validation_reports/w8/5w8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Enzymatic activity assay showed that LpxB with mutations in the swapped portion of the dimer can be complemented by LpxB with mutation in the unswapped portion by forming an LpxB mutant heterodimer with more activity than individual LpxB mutants. Thus, C-terminal swapped dimerization occurs and creates one intact active site in each LpxB mutant heterodimer. |
-Components
#1: Protein | Mass: 42281.875 Da / Num. of mol.: 1 / Mutation: V66S, V68S, L69S, L72S, L75S, L76S, M207S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: lpxB, ECBD_3437 / Plasmid: pE-SUMO Details (production host): cleavable His-tagged N-terminal SUMO Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NAT1, UniProt: P10441*PLUS, lipid-A-disaccharide synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-LI / | #4: 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: 2.45 Å3/Da / Density % sol: 49.86 % / Description: bipyramidal |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 39% PEG 4000, 0.1 M Tris-HCl pH 8.6, 0.7 M LiCl mixed 1:1 with 8 g/L protein in 0.3 M NaCl, 5% glycerol, 20 mM Tris-HCl pH 7.4, 5 mM DTT with 100 mM trimethylammonium chloride additive used ...Details: 39% PEG 4000, 0.1 M Tris-HCl pH 8.6, 0.7 M LiCl mixed 1:1 with 8 g/L protein in 0.3 M NaCl, 5% glycerol, 20 mM Tris-HCl pH 7.4, 5 mM DTT with 100 mM trimethylammonium chloride additive used at 10 mM or 10% of drop volume |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→155.14 Å / Num. obs: 24865 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.041 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2012 / CC1/2: 0.55 / Rpim(I) all: 0.615 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→55.07 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / Phase error: 23.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→55.07 Å
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Refine LS restraints | Type: GEOSTD + MON.LIB. + CDL v1.2 | ||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å
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