+Open data
-Basic information
Entry | Database: PDB / ID: 6d1d | ||||||
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Title | Crystal structure of NDM-1 complexed with compound 6 | ||||||
Components | Metallo-beta-lactamase type 2 | ||||||
Keywords | HYDROLASE/HYDROLASE inhibitor / beta-lactamase / carbapenemase / phosphonate / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 | 6d1d.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d1d.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 6d1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/6d1d ftp://data.pdbj.org/pub/pdb/validation_reports/d1/6d1d | HTTPS FTP |
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-Related structure data
Related structure data | 6d15C 6d16C 6d17C 6d18C 6d19C 6d1aC 6d1bC 6d1cC 6d1eC 6d1fC 6d1gC 6d1hC 6d1iC 6d1jC 6d1kC 6dd0C 6dd1C 6ny7C 6o3rC 6o5tC 4tzfS 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
#1: Protein | Mass: 24602.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GTV / [( | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.89 % |
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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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979193 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979193 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.4→34.22 Å / Num. obs: 37707 / % possible obs: 93.5 % / Redundancy: 3 % / Biso Wilson estimate: 10.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.032 / Rrim(I) all: 0.057 / Rsym value: 0.047 / Net I/σ(I): 12.7 | |||||||||||||||||||||||||||
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: 4TZF Resolution: 1.4→24.319 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 16.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.29 Å2 / Biso mean: 16.653 Å2 / Biso min: 5.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→24.319 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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