+Open data
-Basic information
Entry | Database: PDB / ID: 7ss6 | ||||||
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Title | Structure of Klebsiella LpxH in complex with JH-LPH-45 | ||||||
Components | UDP-2,3-diacylglucosamine hydrolase | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / LpxH / lipid A / antibiotic / Gram-negative bacteria / HYDROLASE-ANTIBIOTIC complex | ||||||
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: 1.74 Å | ||||||
Authors | Cho, J. / Cochrane, C.S. / Zhou, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemmedchem / Year: 2023 Title: Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH. Authors: Kwak, S.H. / Skyler Cochrane, C. / Cho, J. / Dome, P.A. / Ennis, A.F. / Kim, J.H. / Zhou, P. / Hong, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ss6.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ss6.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ss6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ss6_validation.pdf.gz | 721 KB | Display | wwPDB validaton report |
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Full document | 7ss6_full_validation.pdf.gz | 723.8 KB | Display | |
Data in XML | 7ss6_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7ss6_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/7ss6 ftp://data.pdbj.org/pub/pdb/validation_reports/ss/7ss6 | HTTPS FTP |
-Related structure data
Related structure data | 7ss7C 6pj3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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, UDP-2,3-diacylglucosamine diphosphatase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-BKB / | #4: Chemical | ChemComp-EDO / #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: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 4 mg/mL protein, 0.27 mM JH-LPH-45, 10 mM MES (pH 6.0), 100 mM NaCl, 0.5 mM DTT, 2.5% glycerol, 0.625% DMSO, 0.025 M magnesium acetate tetrahydrate, 0.025 M sodium acetate pH 5.4, 12% v/v PEG400 |
-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 / Detector: PIXEL / Date: Nov 25, 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: 1.74→46.28 Å / Num. obs: 35718 / % possible obs: 99.95 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 24.31 |
Reflection shell | Resolution: 1.74→1.8 Å / Num. unique obs: 3542 / CC1/2: 0.934 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PJ3 Resolution: 1.74→46.28 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5452 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→46.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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