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Yorodumi- PDB-5knk: Lipid A secondary acyltransferase LpxM from Acinetobacter baumann... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5knk | ||||||
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Title | Lipid A secondary acyltransferase LpxM from Acinetobacter baumannii with catalytic residue substitution (E127A) | ||||||
Components | Lipid A biosynthesis lauroyl acyltransferase | ||||||
Keywords | TRANSFERASE / LpxM MsbB WaaN / Acyl Transferase / Lauryl Transferase | ||||||
Function / homology | Bacterial lipid A biosynthesis acyltransferase / Bacterial lipid A biosynthesis acyltransferase / glycolipid biosynthetic process / acyltransferase activity / plasma membrane / UNDECANOIC ACID / Lipid A biosynthesis lauroyl acyltransferase Function and homology information | ||||||
Biological species | Acinetobacter baumannii NIPH 410 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Dovala, D.L. / Hu, Q. / Metzger IV, L.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism. Authors: Dovala, D. / Rath, C.M. / Hu, Q. / Sawyer, W.S. / Shia, S. / Elling, R.A. / Knapp, M.S. / Metzger, L.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5knk.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5knk.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 5knk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/5knk ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knk | HTTPS FTP |
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-Related structure data
Related structure data | 5kn7SC 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
-Protein / Sugars , 2 types, 3 molecules B
#1: Protein | Mass: 38133.590 Da / Num. of mol.: 1 / Mutation: E127A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii NIPH 410 (bacteria) Gene: F910_00940 / Production host: Escherichia coli (E. coli) / References: UniProt: S3TFW2 |
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#4: Sugar |
-Non-polymers , 4 types, 113 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #5: Chemical | ChemComp-11A / | #6: 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: 2.56 Å3/Da / Density % sol: 51.94 % / Description: Small guitar pick shaped crystals. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM KBr 2.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→72.74 Å / Num. obs: 30262 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 7.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KN7 Resolution: 1.9→72.735 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.9 Å2 / Biso mean: 32.284 Å2 / Biso min: 10.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→72.735 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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