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Yorodumi- PDB-4ehx: Crystal structure of LpxK from Aquifex aeolicus at 1.9 angstrom r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ehx | ||||||
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Title | Crystal structure of LpxK from Aquifex aeolicus at 1.9 angstrom resolution | ||||||
Components | Tetraacyldisaccharide 4'-kinase | ||||||
Keywords | TRANSFERASE / membrane protein / kinase / lipid A / P-loop / P-loop containing nucleoside triphosphate hydrolase / disaccharide-1-phosphate 4'-kinase / membrane / lipid metabolism / tetraacyldisaccharide 4'-kinase | ||||||
Function / homology | Function and homology information tetraacyldisaccharide 4'-kinase / tetraacyldisaccharide 4'-kinase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Emptage, R.P. / Daughtry, K.D. / Pemble IV, C.W. / Raetz, C.R.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Authors: Emptage, R.P. / Daughtry, K.D. / Pemble, C.W. / Raetz, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ehx.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ehx.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ehx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ehx_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 4ehx_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 4ehx_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4ehx_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/4ehx ftp://data.pdbj.org/pub/pdb/validation_reports/eh/4ehx | HTTPS FTP |
-Related structure data
Related structure data | 4ehwSC 4ehyC 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: 36597.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1656, lpxK / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: O67572, tetraacyldisaccharide 4'-kinase | ||||
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#2: Chemical | ChemComp-EPE / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #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: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop, vapor diffusion / pH: 7.5 Details: The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained ~1 mg/ml protein, 54% MPD, 90 mM Hepes pH 7.5, 2 mM Hepes pH 8.0, 75 mM NaCl, 2% glycerol, ~0.03% DDM, 2 ...Details: The reservoir solution contained 60% MPD and 0.1 M Hepes pH 7.5. The drop contained ~1 mg/ml protein, 54% MPD, 90 mM Hepes pH 7.5, 2 mM Hepes pH 8.0, 75 mM NaCl, 2% glycerol, ~0.03% DDM, 2 mM MgCl2, 0.4 mM AMP-PNP, 0.4 mM methyl-2-acetamido-2-deoxy-B-D-glucopyranoside. hanging drop, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. all: 36583 / Num. obs: 36493 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Χ2: 1.048 / Net I/σ(I): 9.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EHW Resolution: 1.9→23.021 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 0.11 / Phase error: 18.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.707 Å2 / ksol: 0.351 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.24 Å2 / Biso mean: 44.4362 Å2 / Biso min: 13.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→23.021 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: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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