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Open data
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Basic information
Entry | Database: PDB / ID: 5za2 | ||||||||||||
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Title | Fox-4 beta-lactamase complexed with avibactam | ||||||||||||
![]() | (Beta-lactamase![]() | ||||||||||||
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Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Nukaga, M. / Hoshino, T. / Papp-Wallace, K.M. / Bonomo, R.A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Probing the Mechanism of Inactivation of the FOX-4 Cephamycinase by Avibactam Authors: Nukaga, M. / Papp-Wallace, K.M. / Hoshino, T. / Lefurgy, S.T. / Bethel, C.R. / Barnes, M.D. / Zeiser, E.T. / Johnson, J.K. / Bonomo, R.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 | ![]() | 159.2 KB | Display | ![]() |
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PDB format | ![]() | 126.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 38039.973 Da / Num. of mol.: 1 / Fragment: UNP residues 29-382 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 38217.066 Da / Num. of mol.: 1 / Fragment: UNP residues 28-382 Source method: isolated from a genetically manipulated source Details: In molB of the structure, Ser58 was partially phosphorilated. And partially inhibited(cobalently bonded to avibactam(NXL)) Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 536 molecules ![](data/chem/img/NXL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-EPE / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | There are both SEP and Ser at the same position in the chain B. The Ser64 is linked to NXL. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG8000, MOPS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→50 Å / Num. obs: 101610 / % possible obs: 99.2 % / Redundancy: 7.5 % / Net I/σ(I): 14.95 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5036 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.503→37.624 Å
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Refine LS restraints |
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LS refinement shell |
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