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Open data
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Basic information
Entry | Database: PDB / ID: 7cid | ||||||
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Title | Crystal structure of P.aeruginosa LpxC in complex with inhibitor | ||||||
![]() | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
![]() | HYDROLASE / UDP-3-O-acyl-N-acetylglucosamine deacetylase / EnvA / LpxC / Pseudomonas aeruginosa | ||||||
Function / homology | ![]() UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baker, L.M. / Mima, M. / Surgenor, A. / Robertson, A. | ||||||
![]() | ![]() Title: Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity. Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / ...Authors: Yamada, Y. / Takashima, H. / Walmsley, D.L. / Ushiyama, F. / Matsuda, Y. / Kanazawa, H. / Yamaguchi-Sasaki, T. / Tanaka-Yamamoto, N. / Yamagishi, J. / Kurimoto-Tsuruta, R. / Ogata, Y. / Ohtake, N. / Angove, H. / Baker, L. / Harris, R. / Macias, A. / Robertson, A. / Surgenor, A. / Watanabe, H. / Nakano, K. / Mima, M. / Iwamoto, K. / Okada, A. / Takata, I. / Hitaka, K. / Tanaka, A. / Fujita, K. / Sugiyama, H. / Hubbard, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 51.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 692.5 KB | Display | ![]() |
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Full document | ![]() | 693 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ci4C ![]() 7ci5C ![]() 7ci6C ![]() 7ci7C ![]() 7ci8C ![]() 7ci9C ![]() 7ciaC ![]() 7cibC ![]() 7cicC ![]() 7cieC ![]() 3uhmS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase |
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#2: Chemical | ChemComp-FZ3 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG 4K 0.2M MgCl2 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→28.36 Å / Num. obs: 9121 / % possible obs: 90 % / Redundancy: 4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.49→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 645 / CC1/2: 0.848 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UHM Resolution: 2.49→28.37 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.346 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 27.023 Å2
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Refinement step | Cycle: 1 / Resolution: 2.49→28.37 Å
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Refine LS restraints |
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