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Open data
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Basic information
Entry | Database: PDB / ID: 6dd0 | ||||||
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Title | Crystal structure of VIM-2 complexed with compound 8 | ||||||
![]() | Beta-lactamase class B VIM-2 | ||||||
![]() | HYDROLASE / beta-lactamase / carbapenemase / phosphonate / inhibitor | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pemberton, O.A. / Chen, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.3 KB | Display | ![]() |
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PDB format | ![]() | 159.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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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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Components
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2 Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||
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: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() 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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