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- PDB-8sq8: X-ray crystal structure of Acinetobacter baumanii beta-lactamase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sq8 | ||||||
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Title | X-ray crystal structure of Acinetobacter baumanii beta-lactamase variant OXA-109 in complex with doripenem | ||||||
![]() | Beta-lactamase OXA-109 | ||||||
![]() | HYDROLASE/INHIBITOR / ANTIBIOTIC / Acinetobacter beta-lactamase Complex carbapenem Doripenem / HYDROLASE / HYDROLASE-INHIBITOR / ANTIBIOTIC complex | ||||||
Function / homology | Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Chem-4J6 / BICARBONATE ION / Beta-lactamase OXA-109![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Powers, R.A. / Leonard, D.A. / June, C.M. / Szarecka, A. / Wawrzak, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Dynamic Features of Acinetobacter baumannii OXA-66 beta-Lactamase Explain Its Stability and Evolution of Novel Variants. Authors: Klamer, Z.L. / June, C.M. / Wawrzak, Z. / Taracila, M.A. / Grey, J.A. / Benn, A.M.I. / Russell, C.P. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A. / Szarecka, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.5 KB | Display | ![]() |
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PDB format | ![]() | 158.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8sq7C 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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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: 28170.109 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-4J6 / ( #3: Chemical | #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: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.09 M HEPES, pH 7.5, 1.26 M Sodium Citrate, 10% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→30 Å / Num. obs: 59493 / % possible obs: 99.62 % / Redundancy: 7.2 % / CC1/2: 1 / Net I/σ(I): 29.81 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2881 / CC1/2: 0.666 / % possible all: 99.95 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 53.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→29.94 Å
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Refine LS restraints |
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LS refinement shell |
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