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Open data
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Basic information
Entry | Database: PDB / ID: 7t5s | ||||||
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Title | P. aeruginosa LpxA in complex with ligand H16 | ||||||
![]() | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
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Function / homology | ![]() acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sacco, M. / Chen, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis. Authors: Sacco, M.D. / Defrees, K. / Zhang, X. / Lawless, W. / Nwanochie, E. / Balsizer, A. / Darch, S.E. / Renslo, A.R. / Chen, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.7 KB | Display | ![]() |
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PDB format | ![]() | 243.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7t5rC ![]() 7t5xC ![]() 7t5zC ![]() 7t60C ![]() 7t61C ![]() 6uegS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 28048.730 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase #2: Chemical | ChemComp-F3R / #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 1,000, 0.2 M CaOAc, 0.1 M imidazole pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 27, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3→45.46 Å / Num. obs: 25934 / % possible obs: 86.7 % / Redundancy: 4.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.07 / Rrim(I) all: 0.159 / Net I/σ(I): 5.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6ueg Resolution: 3→45.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.877 / SU B: 24.268 / SU ML: 0.413 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.579 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.63 Å2 / Biso mean: 52.365 Å2 / Biso min: 23.61 Å2
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Refinement step | Cycle: final / Resolution: 3→45.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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