+Open data
-Basic information
Entry | Database: PDB / ID: 6dd0 | ||||||
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Title | Crystal structure of VIM-2 complexed with compound 8 | ||||||
Components | Beta-lactamase class B VIM-2 | ||||||
Keywords | HYDROLASE / beta-lactamase / carbapenemase / phosphonate / inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Pemberton, O.A. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dd0.cif.gz | 204.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dd0.ent.gz | 159.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/6dd0 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/6dd0 | HTTPS FTP |
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-Related structure data
Related structure data | 6d15C 6d16C 6d17C 6d18C 6d19C 6d1aC 6d1bC 6d1cC 6d1dC 6d1eC 6d1fC 6d1gC 6d1hC 6d1iC 6d1jC 6d1kC 6dd1C 6ny7C 6o3rC 6o5tC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 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 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-ACT / #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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Calcium acetate, 20% (w/v) PEG 3350, 1 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→33.89 Å / Num. all: 65885 / Num. obs: 65885 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.15 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.281 / Rpim(I) all: 0.174 / Rrim(I) all: 0.332 / Rsym value: 0.281 / Net I/σ(I): 5.9 / Num. measured all: 241046 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.6 %
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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: 1KO3 Resolution: 1.5→31.386 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.59 / Phase error: 23.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.24 Å2 / Biso mean: 16.1283 Å2 / Biso min: 2.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→31.386 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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