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Open data
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Basic information
Entry | Database: PDB / ID: 6i5d | |||||||||
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Title | Crystal structure of an OXA-48 beta-lactamase synthetic mutant | |||||||||
![]() | Beta-lactamase![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zavala, A. / Retailleau, P. / Dabos, L. / Naas, T. / Iorga, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate specificity of an OXA-48 beta-lactamase synthetic mutant Authors: Dabos, L. / Zavala, A. / Dortet, L. / Bonnin, R.A. / Beckstein, O. / Retailleau, P. / Iorga, B.I. / Naas, 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 | ![]() | 230.4 KB | Display | ![]() |
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PDB format | ![]() | 184 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hbrS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 29769.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3729690_05506 Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 408 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / ![]() #3: Chemical | ChemComp-CL / | ![]() #4: Chemical | ChemComp-NO3 / ![]() #5: Chemical | ChemComp-EDO / ![]() #6: Chemical | ChemComp-PEG / | ![]() #7: Chemical | ChemComp-PO4 / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M NaNO3; 20% PEG3350 protein stored at 12.5mg/ml in buffer: Sodium Phosphate 0.1M pH=7.0; K2SO4 50mM |
-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: Apr 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→74.9 Å / Num. obs: 58856 / % possible obs: 97.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.035 / Rrim(I) all: 0.056 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2944 / CC1/2: 0.849 / Rpim(I) all: 0.368 / Rrim(I) all: 0.575 / % possible all: 99.2 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 3HBR Resolution: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.092
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Displacement parameters | Biso mean: 34.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→25.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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