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- PDB-8z5l: Crystal structure of metallo-beta-lactamse, IMP-1, complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8z5l | |||||||||
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Title | Crystal structure of metallo-beta-lactamse, IMP-1, complexed with a quinolinone-based inhibitor | |||||||||
![]() | Metallo-beta-lactamase type 2 | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / beta-lactamase inhibitor / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kamo, T. / Kuroda, K. / Nimura, S. / Guo, Y. / Kondo, S. / Nukaga, M. / Hoshino, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of Inhibitory Compounds for Metallo-beta-lactamase through Computational Design and Crystallographic Analysis. Authors: Kamo, T. / Kuroda, K. / Nimura, S. / Guo, Y. / Kondo, S. / Nukaga, M. / Hoshino, 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 | ![]() | 189.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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3 |
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4 |
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Unit cell |
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Components
#1: Protein | Mass: 25685.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | Mass: 438.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H38N2O3 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM HEPES, 15%(W/V) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45.52 Å / Num. obs: 29377 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.073 / Rrim(I) all: 0.176 / Χ2: 1.07 / Net I/σ(I): 10.5 / Num. measured all: 180450 |
Reflection shell | Resolution: 2.65→2.78 Å / % possible obs: 98.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.083 / Num. measured all: 23066 / Num. unique obs: 3809 / CC1/2: 0.705 / Rpim(I) all: 0.483 / Rrim(I) all: 1.189 / Χ2: 0.96 / Net I/σ(I) obs: 1.8 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→43.3 Å
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Refine LS restraints |
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LS refinement shell |
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