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- PDB-8tmt: Crystal structure of KPC-44 carbapenemase in complex with vaborbactam -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tmt | |||||||||
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Title | Crystal structure of KPC-44 carbapenemase in complex with vaborbactam | |||||||||
![]() | beta-lactamase | |||||||||
![]() | HYDROLASE / KPC carbapenemase / ceftazidime-avibactam resistance | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sun, Z. / Palzkill, T. / Hu, L. / Neetu, N. / Lin, H. / Sankaran, B. / Wang, J. / Prasad, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops. Authors: Sun, Z. / Lin, H. / Hu, L. / Neetu, N. / Sankaran, B. / Wang, J. / Prasad, B.V.V. / Palzkill, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.8 KB | Display | ![]() |
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Full document | ![]() | 858.1 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tjmC ![]() 8tmrC ![]() 8tn0C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30035.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 310 molecules ![](data/chem/img/4D6.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/LI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4D6 / | ||||||||
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#3: Chemical | ChemComp-GOL / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | ChemComp-LI / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.2 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.0-4.4, and 22-24% (w/v) PEG 1000 PH range: 4.0 - 4.4 / Temp details: 25oc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50.553 Å / Num. obs: 29050 / % possible obs: 100 % / Redundancy: 10.58 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 5 / Num. unique obs: 4184 / CC1/2: 0.926 / Rpim(I) all: 0.154 / Rrim(I) all: 0.506 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50.553 Å
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Refine LS restraints |
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LS refinement shell |
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