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- PDB-5ew0: Crystal structure of the metallo-beta-lactamase Sfh-I in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ew0 | ||||||
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Title | Crystal structure of the metallo-beta-lactamase Sfh-I in complex with the bisthiazolidine inhibitor L-CS319 | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / inhibitor / carbapenemase / antibiotic resistance | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hinchliffe, P. / Tooke, C.L. / Spencer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cross-class metallo-beta-lactamase inhibition by bisthiazolidines reveals multiple binding modes. Authors: Hinchliffe, P. / Gonzalez, M.M. / Mojica, M.F. / Gonzalez, J.M. / Castillo, V. / Saiz, C. / Kosmopoulou, M. / Tooke, C.L. / Llarrull, L.I. / Mahler, G. / Bonomo, R.A. / Vila, A.J. / Spencer, 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 | ![]() | 208.6 KB | Display | ![]() |
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PDB format | ![]() | 165.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nq6C ![]() 5ev6C ![]() 5ev8C ![]() 5evbC ![]() 5evdC ![]() 5evkC ![]() 5ewaC ![]() 3sd9S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 41 - 268 / Label seq-ID: 6 - 233
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Components
#1: Protein | Mass: 26317.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium acetate, 27% w/v PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.3→19.42 Å / Num. obs: 91618 / % possible obs: 97.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.6 | |||||||||||||||
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.2 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SD9 Resolution: 1.3→19.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.192 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.754 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→19.42 Å
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Refine LS restraints |
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