+Open data
-Basic information
Entry | Database: PDB / ID: 6mnp | ||||||
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Title | Crystal structure of KPC-2 with compound 6 | ||||||
Components | Carbapenem-hydrolyzing beta-lactamase KPC | ||||||
Keywords | HYDROLASE/INHIBITOR / Carbapenemase / tetrazole / inhibitor / complex / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 Å | ||||||
Authors | Akhtar, A. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mnp.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mnp.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 6mnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mnp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6mnp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6mnp_validation.xml.gz | 12 KB | Display | |
Data in CIF | 6mnp_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/6mnp ftp://data.pdbj.org/pub/pdb/validation_reports/mn/6mnp | HTTPS FTP |
-Related structure data
Related structure data | 6efjC 6m7iC 6md8C 6mduC 6meyC 6miaC 6mllC 3c5aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30806.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, kpc, kpc1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F663, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 5% (v/v) Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 13530 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.072 / Rrim(I) all: 0.155 / Χ2: 1.082 / Net I/σ(I): 6.8 / Num. measured all: 66050 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3C5A Resolution: 2.202→47.236 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.29 Å2 / Biso mean: 45.8964 Å2 / Biso min: 28.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.202→47.236 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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