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Yorodumi- PDB-7ojy: Crystal structure of Pseudomonas aeruginosa LpxA in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ojy | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 6 | ||||||
Components | Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase | ||||||
Keywords | TRANSFERASE / ACYLTRANSFERASE / FATTY ACIDS / LIPID A / LEFT-HANDED PARALLEL BETA-HELIX | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ryan, M.D. / Parkes, A.L. / Southey, M. / Andersen, O.A. / Zahn, M. / Barker, J. / DeJonge, B.L.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ojy.cif.gz | 320.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojy.ent.gz | 259.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ojy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ojy_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7ojy_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7ojy_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 7ojy_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojy ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojy | HTTPS FTP |
-Related structure data
Related structure data | 7oj6C 7ojpC 7ojqC 7ojwC 7ok1C 7ok2C 7okaC 7okbC 7okcC 5demS 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: 28331.010 Da / Num. of mol.: 3 / Fragment: full-length protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria) Strain: PA7 / Gene: lpxA, PSPA7_1495 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS References: UniProt: A6V1E4, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→83.2 Å / Num. obs: 91413 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.067 / Rrim(I) all: 0.175 / Net I/σ(I): 4.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DEM Resolution: 2→58.83 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.117
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Displacement parameters | Biso max: 133.03 Å2 / Biso mean: 48.35 Å2 / Biso min: 26.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→58.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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