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- PDB-7oj6: Crystal structure of Pseudomonas aeruginosa LpxA in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oj6 | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 1 | ||||||
![]() | Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase | ||||||
![]() | TRANSFERASE / ACYLTRANSFERASE / FATTY ACIDS / LIPID A / LEFT-HANDED PARALLEL BETA-HELIX | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ryan, M.D. / Parkes, A.L. / Southey, M. / Andersen, O.A. / Zahn, M. / Barker, J. / DeJonge, B.L.M. | ||||||
![]() | ![]() Title: Discovery of Novel UDP- N -Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa . Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, ...Authors: Ryan, M.D. / Parkes, A.L. / Corbett, D. / Dickie, A.P. / Southey, M. / Andersen, O.A. / Stein, D.B. / Barbeau, O.R. / Sanzone, A. / Thommes, P. / Barker, J. / Cain, R. / Compper, C. / Dejob, M. / Dorali, A. / Etheridge, D. / Evans, S. / Faulkner, A. / Gadouleau, E. / Gorman, T. / Haase, D. / Holbrow-Wilshaw, M. / Krulle, T. / Li, X. / Lumley, C. / Mertins, B. / Napier, S. / Odedra, R. / Papadopoulos, K. / Roumpelakis, V. / Spear, K. / Trimby, E. / Williams, J. / Zahn, M. / Keefe, A.D. / Zhang, Y. / Soutter, H.T. / Centrella, P.A. / Clark, M.A. / Cuozzo, J.W. / Dumelin, C.E. / Deng, B. / Hunt, A. / Sigel, E.A. / Troast, D.M. / DeJonge, B.L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.3 KB | Display | ![]() |
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PDB format | ![]() | 266.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 56.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ojpC ![]() 7ojqC ![]() 7ojwC ![]() 7ojyC ![]() 7ok1C ![]() 7ok2C ![]() 7okaC ![]() 7okbC ![]() 7okcC ![]() 5demS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 258 / Label seq-ID: 4 - 261
NCS ensembles :
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Components
#1: Protein | Mass: 28331.010 Da / Num. of mol.: 3 / Fragment: full-length protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PA7 / Gene: lpxA, PSPA7_1495 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: 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: 4.05 Å3/Da / Density % sol: 69.6 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5 M NH4Cl, 0.1 M Na Acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→59.52 Å / Num. obs: 114341 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 29.032 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.051 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 1 / Num. unique obs: 4717 / CC1/2: 0.593 / Rpim(I) all: 0.564 / Rrim(I) all: 0.921 / % possible all: 80.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DEM Resolution: 1.84→59.52 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.022 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 143.78 Å2 / Biso mean: 45.042 Å2 / Biso min: 23.83 Å2
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Refinement step | Cycle: final / Resolution: 1.84→59.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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