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Open data
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Basic information
Entry | Database: PDB / ID: 7khq | ||||||
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Title | Crystal structure of OXA-48 K73A in complex with meropenem | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / beta-lactamase / carbapenemase / beta-lactamase inhibitor / complex / oxacillinase / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palzkill, T. / Hu, L. / Sankaran, B. / Prasad, B.V.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic Basis of OXA-48-like beta-Lactamases' Hydrolysis of Carbapenems. Authors: Stojanoski, V. / Hu, L. / Sankaran, B. / Wang, F. / Tao, P. / 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 | ![]() | 146.1 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kh9C ![]() 7khyC ![]() 7khzC ![]() 3hbrS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28193.947 Da / Num. of mol.: 2 / Mutation: K73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bla OXA-48, bla_2, bla_3, blaOXA-48, B6R99_29845, G5637_27540, GJJ01_28680, KPE71T_00045, SAMEA3649466_05396, SAMEA3673128_05462, SAMEA3729780_05587 Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: 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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 200 mM lithium acetate dihydrate and 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2014 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.24 Å / Num. obs: 40232 / % possible obs: 99.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 2→2.04 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1925 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HBR Resolution: 2→34.24 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.509 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.24 Å
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Refine LS restraints |
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LS refinement shell |
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