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Open data
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Basic information
Entry | Database: PDB / ID: 6d1f | ||||||
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Title | Crystal structure of NDM-1 complexed with compound 8 | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE/HYDROLASE inhibitor / beta-lactamase / carbapenemase / phosphonate / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc 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 | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6d15C ![]() 6d16C ![]() 6d17C ![]() 6d18C ![]() 6d19C ![]() 6d1aC ![]() 6d1bC ![]() 6d1cC ![]() 6d1dC ![]() 6d1eC ![]() 6d1gC ![]() 6d1hC ![]() 6d1iC ![]() 6d1jC ![]() 6d1kC ![]() 6dd0C ![]() 6dd1C ![]() 6ny7C ![]() 6o3rC ![]() 6o5tC ![]() 4tzfS 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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Unit cell |
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Components
#1: Protein | Mass: 24602.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-P9T / [( | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 50 mM Potassium phosphate monobasic, 10 mM Calcium chloride, 25% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.15→27.84 Å / Num. obs: 72080 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.048 / Rrim(I) all: 0.093 / Rsym value: 0.079 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 4TZF Resolution: 1.15→27.32 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 16.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.72 Å2 / Biso mean: 15.3124 Å2 / Biso min: 4.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→27.32 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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