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Yorodumi- PDB-5mm9: VIM-2_2b. Metallo-beta-Lactamase Inhibitors by Bioisosteric Repla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mm9 | ||||||
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Title | VIM-2_2b. Metallo-beta-Lactamase Inhibitors by Bioisosteric Replacement: Preparation, Activity and Binding | ||||||
Components | Metallo-beta-lactamase VIM-17 | ||||||
Keywords | HYDROLASE / inhibition properties / bioisosters / thiols / metallo-beta-lactamase inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Skagseth, S. / Akhter, S. / Paulsen, M.H. / Samuelsen, O. / Muhammad, Z. / Leiros, H.-K.S. / Bayer, A. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Eur J Med Chem / Year: 2017 Title: Metallo-beta-lactamase inhibitors by bioisosteric replacement: Preparation, activity and binding. Authors: Skagseth, S. / Akhter, S. / Paulsen, M.H. / Muhammad, Z. / Lauksund, S. / Leiros, H.S. / Bayer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mm9.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mm9.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/5mm9 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/5mm9 | HTTPS FTP |
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-Related structure data
Related structure data | 5nhzC 5ni0C 5lscS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25596.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star pLysS / References: UniProt: B5KVR9 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 22-27 percent polyethylene glycol PEG 3350 0.2 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25 Å / Num. obs: 54949 / % possible obs: 93.58 % / Redundancy: 2 % / Biso Wilson estimate: 14.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.16 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.91 / CC1/2: 0.679 / % possible all: 92.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5lsc Resolution: 1.55→25 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→25 Å
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Refine LS restraints |
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LS refinement shell |
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