+Open data
-Basic information
Entry | Database: PDB / ID: 6p9p | ||||||
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Title | E.coli LpxA in complex with Compound 1 | ||||||
Components | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase | ||||||
Keywords | TRANSFERASE/INHIBITOR / Acyltransferase / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||
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 / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ma, X. / Shia, S. / Ornelas, E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis. Authors: Han, W. / Ma, X. / Balibar, C.J. / Baxter Rath, C.M. / Benton, B. / Bermingham, A. / Casey, F. / Chie-Leon, B. / Cho, M.K. / Frank, A.O. / Frommlet, A. / Ho, C.M. / Lee, P.S. / Li, M. / ...Authors: Han, W. / Ma, X. / Balibar, C.J. / Baxter Rath, C.M. / Benton, B. / Bermingham, A. / Casey, F. / Chie-Leon, B. / Cho, M.K. / Frank, A.O. / Frommlet, A. / Ho, C.M. / Lee, P.S. / Li, M. / Lingel, A. / Ma, S. / Merritt, H. / Ornelas, E. / De Pascale, G. / Prathapam, R. / Prosen, K.R. / Rasper, D. / Ruzin, A. / Sawyer, W.S. / Shaul, J. / Shen, X. / Shia, S. / Steffek, M. / Subramanian, S. / Vo, J. / Wang, F. / Wartchow, C. / Uehara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p9p.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p9p.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p9p_validation.pdf.gz | 694.4 KB | Display | wwPDB validaton report |
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Full document | 6p9p_full_validation.pdf.gz | 694.7 KB | Display | |
Data in XML | 6p9p_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6p9p_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/6p9p ftp://data.pdbj.org/pub/pdb/validation_reports/p9/6p9p | HTTPS FTP |
-Related structure data
Related structure data | 6p9qC 6p9rC 6p9sC 6p9tC 1lxaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28945.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxA, EC958_0327 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: W9AB79, UniProt: P0A722*PLUS, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-O5J / | #5: 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: 2.63 Å3/Da / Density % sol: 53.2 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na/K phosphate, 10% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→48.11 Å / Num. obs: 20275 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Rrim(I) all: 0.143 / Net I/σ(I): 8.5 / Num. measured all: 72097 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LXA Resolution: 2→43.034 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.37 Å2 / Biso mean: 34.5254 Å2 / Biso min: 16.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→43.034 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 26.935 Å / Origin y: -3.903 Å / Origin z: -5.052 Å
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Refinement TLS group |
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