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Open data
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Basic information
Entry | Database: PDB / ID: 6efj | ||||||
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Title | Crystal structure of NDM-1 with compound 9 | ||||||
![]() | Metallo-beta-lactamase type 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Akhtar, A. / Chen, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. Authors: Torelli, N.J. / Akhtar, A. / DeFrees, K. / Jaishankar, P. / Pemberton, O.A. / Zhang, X. / Johnson, C. / 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 | ![]() | 66.5 KB | Display | ![]() |
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PDB format | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6m7iC ![]() 6md8C ![]() 6mduC ![]() 6meyC ![]() 6miaC ![]() 6mllC ![]() 6mnpC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24602.680 Da / Num. of mol.: 1 / Fragment: residues 42-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-O5E / ( | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05 M Potassium Phosphate, 0.01 M Calcium Chloride, 25%(w/v) PEG-8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.65→33.97 Å / Num. obs: 22276 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Rsym value: 0.101 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||
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: 1.65→33.967 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.84 Å2 / Biso mean: 16.8523 Å2 / Biso min: 4.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→33.967 Å
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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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