+Open data
-Basic information
Entry | Database: PDB / ID: 7ci5 | ||||||
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Title | Crystal structure of P.aeruginosa LpxC in complex with inhibitor | ||||||
Components | UDP-3-O-acyl-N-acetylglucosamine deacetylase | ||||||
Keywords | HYDROLASE / UDP-3-O-acyl-N-acetylglucosamine deacetylase / EnvA / LpxC / Pseudomonas aeruginosa | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mima, M. / Baker, L.M. / Surgenor, A. / Robertson, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ci5.cif.gz | 238.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ci5.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ci5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ci5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ci5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ci5_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 7ci5_validation.cif.gz | 60.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/7ci5 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/7ci5 | HTTPS FTP |
-Related structure data
Related structure data | 7ci4C 7ci6C 7ci7C 7ci8C 7ci9C 7ciaC 7cibC 7cicC 7cidC 7cieC 3uhmS 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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Unit cell |
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-Components
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 4 / Mutation: C40S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli (E. coli) References: UniProt: P47205, UDP-3-O-acyl-N-acetylglucosamine deacetylase #2: Chemical | ChemComp-FXX / ( #3: Chemical | ChemComp-MPO / #4: Chemical | ChemComp-ZN / #5: 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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.02M 1,6-Hexanediol 0.02M 1-Butanol 0.02M 1,2-Propanediol 0.02M 2-Propanol 0.02M 1,4-Butanediol 0.02M 1,3-Propanediol 0.1M Sodium HEPES - MOPS pH 7.5 20 % v/v PEG 500 MME 10 % w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→22.78 Å / Num. obs: 40242 / % possible obs: 96.4 % / Redundancy: 3.28 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3 / Num. unique obs: 3920 / % possible all: 94.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UHM Resolution: 2.5→22.78 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 13.521 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / 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: 38.279 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→22.78 Å
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