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Yorodumi- PDB-6j8r: Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j8r | ||||||
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Title | Metallo-Beta-Lactamase VIM-2 in complex with Dual MBL/SBL Inhibitor MS01 | ||||||
Components | Beta-lactamase class B VIM-2 | ||||||
Keywords | HYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2 | ||||||
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 / molecular replacement / Resolution: 1.575 Å | ||||||
Authors | Li, G.-B. / Liu, S. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases. Authors: Wang, Y.L. / Liu, S. / Yu, Z.J. / Lei, Y. / Huang, M.Y. / Yan, Y.H. / Ma, Q. / Zheng, Y. / Deng, H. / Sun, Y. / Wu, C. / Yu, Y. / Chen, Q. / Wang, Z. / Wu, Y. / Li, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j8r.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j8r.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j8r_validation.pdf.gz | 822 KB | Display | wwPDB validaton report |
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Full document | 6j8r_full_validation.pdf.gz | 822.6 KB | Display | |
Data in XML | 6j8r_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6j8r_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/6j8r ftp://data.pdbj.org/pub/pdb/validation_reports/j8/6j8r | HTTPS FTP |
-Related structure data
Related structure data | 6j8qC 6jn3C 6jn4C 6jn5C 6jn6C 5lcaS 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 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, VIM-2, vim-2, IPC669_36195 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 |
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-Non-polymers , 5 types, 236 molecules
#2: Chemical | #3: Chemical | ChemComp-BHU / [[( | #4: Chemical | ChemComp-FMT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Magnesium Formate, 21%-27% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jun 1, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→50 Å / Num. obs: 36585 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.073 / Rrim(I) all: 0.264 / Χ2: 0.957 / Net I/σ(I): 5.8 / Num. measured all: 401008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LCA Resolution: 1.575→48.169 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.76 Å2 / Biso mean: 18.1487 Å2 / Biso min: 5.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.575→48.169 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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