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- PDB-8ek9: Crystal structure of the class A carbapenemase CRH-1 in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ek9 | |||||||||
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Title | Crystal structure of the class A carbapenemase CRH-1 in complex with avibactam at 1.4 Angstrom resolution | |||||||||
![]() | Beta-lactamase | |||||||||
![]() | ANTIMICROBIAL PROTEIN / class A carbapenemase / environmental lactamase / Chromobacterium / DBO inhibitor | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Power, P. / Brunetti, F. / Ghiglione, B. / Guardabassi, L. / Gutkind, G. / Klinke, S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC beta-Lactamases. Authors: Brunetti, F. / Ghiglione, B. / Gudeta, D.D. / Gutkind, G. / Guardabassi, L. / Klinke, S. / Power, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.3 KB | Display | ![]() |
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Full document | ![]() | 789.9 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ehuC ![]() 4eqiS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28685.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: B0T45_03570 / Plasmid: pET28a / Production host: ![]() ![]() |
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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: 2.42 Å3/Da / Density % sol: 49 % / Description: rectangular prisms |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 22% (w/v) PEG 4,000 + 0.2 M lithium chloride + 0.1 M Tris-HCl pH 7.6 |
-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: Oct 16, 2021 Details: convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors |
Radiation | Monochromator: Cryogenically cooled channel cut crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885601 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→42.22 Å / Num. obs: 53514 / % possible obs: 99.6 % / Redundancy: 6.87 % / Biso Wilson estimate: 23.83 Å2 / CC1/2: 1 / Rrim(I) all: 0.033 / Net I/σ(I): 24.24 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 6.82 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 8539 / CC1/2: 0.814 / Rrim(I) all: 1.007 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EQI Resolution: 1.4→42.22 Å / SU ML: 0.2003 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.8232 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: 31.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→42.22 Å
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Refine LS restraints |
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LS refinement shell |
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