+Open data
-Basic information
Entry | Database: PDB / ID: 7cia | ||||||
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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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 | 7cia.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cia.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cia_validation.pdf.gz | 883.4 KB | Display | wwPDB validaton report |
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Full document | 7cia_full_validation.pdf.gz | 872.7 KB | Display | |
Data in XML | 7cia_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 7cia_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/7cia ftp://data.pdbj.org/pub/pdb/validation_reports/ci/7cia | HTTPS FTP |
-Related structure data
Related structure data | 7ci4C 7ci5C 7ci6C 7ci7C 7ci8C 7ci9C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33146.617 Da / Num. of mol.: 1 / 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS pH 8.5 30% Polyethylene glycol 4K 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→19.5 Å / Num. obs: 20142 / % possible obs: 95 % / Redundancy: 4.78 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.16 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 738 / % possible all: 48.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UHM Resolution: 1.92→19.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.65 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.155 / 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: 20.966 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→19.5 Å
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Refine LS restraints |
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