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- PDB-8g2r: CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH AVIBACTAM -
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Open data
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Basic information
Entry | Database: PDB / ID: 8g2r | ||||||
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Title | CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH AVIBACTAM | ||||||
![]() | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
![]() | HYDROLASE/Antibiotic / Beta-lactamase / inhibitor / antibiotic resistance / HYDROLASE / HYDROLASE-Antibiotic complex | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alsenani, T. / van den Akker, F. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.9 KB | Display | ![]() |
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Full document | ![]() | 788 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g2tC ![]() 2ov5S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28175.754 Da / Num. of mol.: 1 / Mutation: D179N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NXL / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M sodium acetate pH 6, 1.25 M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→49.06 Å / Num. obs: 60468 / % possible obs: 92.8 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 3.026 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3133 / CC1/2: 0.361 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OV5 Resolution: 1.28→49.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.164 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 96.97 Å2 / Biso mean: 20.609 Å2 / Biso min: 6.13 Å2
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Refinement step | Cycle: final / Resolution: 1.28→49.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.311 Å / Rfactor Rfree error: 0
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