+Open data
-Basic information
Entry | Database: PDB / ID: 7cic | ||||||
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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-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Baker, L.M. / Mima, 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 | 7cic.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cic.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cic_validation.pdf.gz | 921.1 KB | Display | wwPDB validaton report |
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Full document | 7cic_full_validation.pdf.gz | 925.1 KB | Display | |
Data in XML | 7cic_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 7cic_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/7cic ftp://data.pdbj.org/pub/pdb/validation_reports/ci/7cic | HTTPS FTP |
-Related structure data
Related structure data | 7ci4C 7ci5C 7ci6C 7ci7C 7ci8C 7ci9C 7ciaC 7cibC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 2 / Mutation: C30S 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 | #3: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Morpheus HT-96 (MD1-47). Well A9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→43.93 Å / Num. obs: 59205 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4339 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UHM Resolution: 1.78→43.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.538 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.129 / 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: 30.416 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→43.93 Å
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