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Open data
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Basic information
Entry | Database: PDB / ID: 8cul | ||||||
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Title | Xray ray crystal structure of OXA-24/40 in complex with CR167 | ||||||
![]() | Beta-lactamase | ||||||
![]() | Hydrolase/Inhibitor / carbapenemase / BATSI / inhibitor / HYDROLASE / Hydrolase-Inhibitor complex | ||||||
Function / homology | ![]() penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fernando, M.C. / Wallar, B.J. / Powers, R.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat ...Title: Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii . Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / ...Authors: Introvigne, M.L. / Beardsley, T.J. / Fernando, M.C. / Leonard, D.A. / Wallar, B.J. / Rudin, S.D. / Taracila, M.A. / Rather, P.N. / Colquhoun, J.M. / Song, S. / Fini, F. / Hujer, K.M. / Hujer, A.M. / Prati, F. / Powers, R.A. / Bonomo, R.A. / Caselli, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 811.8 KB | Display | ![]() |
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Full document | ![]() | 813.8 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cumC ![]() 8cuoC ![]() 8cupC ![]() 8cuqC ![]() 3paeS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 27717.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40, SI89_16690 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-0N3 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium, pH 7.5, 2% v/v PEG 400, 2.0 M ammonium sulfate |
-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: Jul 17, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.01→72.54 Å / Num. obs: 26105 / % possible obs: 93.8 % / Redundancy: 7.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.073 / Rrim(I) all: 0.198 / Net I/σ(I): 7.6 | |||||||||||||||||||||||||||
Reflection shell | Num. unique obs: 1305 / Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PAE Resolution: 2.01→72.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.768 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.99 Å2 / Biso mean: 39.43 Å2 / Biso min: 21.38 Å2
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Refinement step | Cycle: final / Resolution: 2.01→72.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.013→2.065 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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