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Yorodumi- PDB-6pj3: Crystal structure of the Klebsiella pneumoniae LpxH/JH-LPH-33 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pj3 | |||||||||
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Title | Crystal structure of the Klebsiella pneumoniae LpxH/JH-LPH-33 complex | |||||||||
Components | UDP-2,3-diacylglucosamine hydrolase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / LpxH / lipid A / JH-LPH-33 | |||||||||
Function / homology | Function and homology information UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Cho, J. / Zhou, P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics. Authors: Cho, J. / Lee, M. / Cochrane, C.S. / Webster, C.G. / Fenton, B.A. / Zhao, J. / Hong, J. / Zhou, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pj3.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pj3.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pj3_validation.pdf.gz | 357 KB | Display | wwPDB validaton report |
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Full document | 6pj3_full_validation.pdf.gz | 358.5 KB | Display | |
Data in XML | 6pj3_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 6pj3_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/6pj3 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/6pj3 | HTTPS FTP |
-Related structure data
Related structure data | 6ph9C 6pibC 5k8kS 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: 29627.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: lpxH_1, lpxH, C3483_19950, NCTC9128_00880, SAMEA104305404_03891 Production host: Escherichia coli (E. coli) References: UniProt: A0A1S0WIC1, UniProt: A6T5R0*PLUS, UDP-2,3-diacylglucosamine diphosphatase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-OKY / | #4: Chemical | #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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10 mM MES, pH 6.0, 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.75% DMSO,25 mM sodium chloride, 10 mM magnesium chloride hexahydrate, 50 mM sodium citrate, pH 6.0, 11% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.81 Å / Num. obs: 16571 / % possible obs: 99.65 % / Redundancy: 8.6 % / Net I/σ(I): 15.19 |
Reflection shell | Resolution: 2.25→2.33 Å / Num. unique obs: 1620 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5k8k Resolution: 2.25→45.81 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→45.81 Å
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Refine LS restraints |
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LS refinement shell |
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