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- PDB-6ewe: Crystal structure of BCII Metallo-beta-lactamase in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ewe | |||||||||
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Title | Crystal structure of BCII Metallo-beta-lactamase in complex with DZ-308 | |||||||||
![]() | Metallo-beta-lactamase type 2 | |||||||||
![]() | HYDROLASE / ANTIMICROBIAL RESISTANCE / METALLO BETA LACTAMASE / INHIBITOR | |||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Stepanovs, D. / McDonough, M.A. / Schofield, C.J. / Zhang, D. / El-Husseiny, A. / Brem, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases. Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. ...Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. / McDonough, M.A. / Schofield, C.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 85 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jmxC ![]() 6eumC ![]() 6ew3C ![]() 6f2nC ![]() 4tytS C: citing same article ( 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24995.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 171 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C0W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C0W.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-C0W / (~{ | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1MM TCEP, 5MM DZ-305, 50MM HEPES PH7.5, 100MM NACL, 0.1MM ZNCL2, 0.1M MAGNESIUM FORMATE, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2016 / Details: mirrors |
Radiation | Monochromator: Double crystal SiIII / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→35.31 Å / Num. obs: 38243 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.46→1.5 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.544 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2839 / CC1/2: 0.44 / Rpim(I) all: 0.724 / Rrim(I) all: 1.845 / % possible all: 98.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TYT Resolution: 1.46→35.308 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.26 Å2 / Biso mean: 29.4366 Å2 / Biso min: 14.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.46→35.308 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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