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Yorodumi- PDB-5mxq: Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mxq | ||||||
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Title | Crystal Structure of the Acquired VIM-2 Metallo-beta-Lactamase in Complex with ANT-90 Inhibitor | ||||||
Components | Beta-lactamase VIM-2 | ||||||
Keywords | HYDROLASE / metallo-beta-lactamase fold / zinc-dependent hydrolase / PFam00753 / alpha-beta-beta-alpha sandwich / metallo-beta-lactamase inhibitor | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Docquier, J.D. / De Luca, F. / Benvenuti, M. / Di Pisa, F. / Pozzi, C. / Mangani, S. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2019 Title: SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy ...Title: SAR Studies Leading to the Identification of a Novel Series of Metallo-beta-lactamase Inhibitors for the Treatment of Carbapenem-Resistant Enterobacteriaceae Infections That Display Efficacy in an Animal Infection Model. Authors: Leiris, S. / Coelho, A. / Castandet, J. / Bayet, M. / Lozano, C. / Bougnon, J. / Bousquet, J. / Everett, M. / Lemonnier, M. / Sprynski, N. / Zalacain, M. / Pallin, T.D. / Cramp, M.C. / ...Authors: Leiris, S. / Coelho, A. / Castandet, J. / Bayet, M. / Lozano, C. / Bougnon, J. / Bousquet, J. / Everett, M. / Lemonnier, M. / Sprynski, N. / Zalacain, M. / Pallin, T.D. / Cramp, M.C. / Jennings, N. / Raphy, G. / Jones, M.W. / Pattipati, R. / Shankar, B. / Sivasubrahmanyam, R. / Soodhagani, A.K. / Juventhala, R.R. / Pottabathini, N. / Pothukanuri, S. / Benvenuti, M. / Pozzi, C. / Mangani, S. / De Luca, F. / Cerboni, G. / Docquier, J.D. / Davies, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mxq.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mxq.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mxq_validation.pdf.gz | 827.8 KB | Display | wwPDB validaton report |
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Full document | 5mxq_full_validation.pdf.gz | 829.7 KB | Display | |
Data in XML | 5mxq_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5mxq_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/5mxq ftp://data.pdbj.org/pub/pdb/validation_reports/mx/5mxq | HTTPS FTP |
-Related structure data
Related structure data | 5mxrC 6hf5C 1ko3S 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24679.439 Da / Num. of mol.: 1 / Fragment: VIM-2 mature protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Plasmid: pET-9a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 |
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-Non-polymers , 5 types, 83 molecules
#2: Chemical | #3: Chemical | ChemComp-U8K / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: 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: 2.13 Å3/Da / Density % sol: 42.22 % / Mosaicity: 0.84 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M cacodylate, 0.2 M Na-acetate, 5 mM DTT, 26% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2014 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→31.38 Å / Num. obs: 14585 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Net I/σ(I): 9.8 / Num. measured all: 91927 / Scaling rejects: 26 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KO3 Resolution: 2→31.09 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.712 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 82.95 Å2 / Biso mean: 26.195 Å2 / Biso min: 12.06 Å2
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Refinement step | Cycle: final / Resolution: 2→31.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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