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- PDB-6skq: OXA-655_MEM. Structural insights into the enhanced carbapenemase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6skq | ||||||
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Title | OXA-655_MEM. Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10. | ||||||
![]() | Beta-lactamase | ||||||
![]() | ANTIBIOTIC / Class D beta-lactamase / crystal structures / Carbapenemases / Antibiotic resistance | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leiros, H.-K.S. | ||||||
![]() | ![]() Title: Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10. Authors: Leiros, H.S. / Thomassen, A.M. / Samuelsen, O. / Flach, C.F. / Kotsakis, S.D. / Larsson, D.G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 491.5 KB | Display | ![]() |
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PDB format | ![]() | 330.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 71.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6skpC ![]() 6skrC ![]() 4s2oS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29625.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MER / ( #3: Chemical | ChemComp-SO4 / #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: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 6.8 mg/mL, 20-23% PEG 3350 0.2 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 61827 / % possible obs: 94.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.979 / Rrim(I) all: 0.185 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.1→2.15 Å / Num. unique obs: 4483 / CC1/2: 0.539 / Rrim(I) all: 0.824 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4s2o Resolution: 2.1→24.05 Å / SU ML: 0.2467 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5815
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.05 Å
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Refine LS restraints |
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LS refinement shell |
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