[English] 日本語
Yorodumi- PDB-8g2t: CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g2t | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELEBACTAM (IMINE HYDROLYSIS INTERMEDIATE) | ||||||
Components | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
Keywords | HYDROLASE/Inhibitor / Beta-lactamase / inhibitor / antibiotic resistance / HYDROLASE / HYDROLASE-Inhibitor complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Alsenani, T. / van den Akker, F. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2023 Title: Exploring avibactam and relebactam inhibition of Klebsiella pneumoniae carbapenemase D179N variant: role of the Omega loop-held deacylation water. Authors: Alsenani, T.A. / Viviani, S.L. / Papp-Wallace, K.M. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8g2t.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8g2t.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 8g2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/8g2t ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2t | HTTPS FTP |
---|
-Related structure data
Related structure data | 8g2rC 2ov5S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28175.754 Da / Num. of mol.: 1 / Mutation: D179N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F663, beta-lactamase |
---|---|
#2: Chemical | ChemComp-YOZ / ( |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM HEPES pH 8.0 and 0.8 M NaH2PO4, 0.8 M KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→29.63 Å / Num. obs: 66874 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.26→1.29 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4781 / CC1/2: 0.931 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OV5 Resolution: 1.26→27.76 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.598 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.705 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.26→27.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|