+Open data
-Basic information
Entry | Database: PDB / ID: 6qwe | ||||||
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Title | Crystal structure of KPC-4 | ||||||
Components | Beta-lactamase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antibiotic resistance / serine beta-lactamase | ||||||
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 / Resolution: 1.4 Å | ||||||
Authors | Tooke, C.L. / Hinchliffe, P. / Spencer, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: Molecular Basis of Class A beta-Lactamase Inhibition by Relebactam. Authors: Tooke, C.L. / Hinchliffe, P. / Lang, P.A. / Mulholland, A.J. / Brem, J. / Schofield, C.J. / Spencer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qwe.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qwe.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qwe_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 6qwe_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 6qwe_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 6qwe_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/6qwe ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qwe | HTTPS FTP |
-Related structure data
Related structure data | 6qw7C 6qw8C 6qw9C 6qwaC 6qwbC 6qwcC 6qwdC 5ul8S 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: 30824.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC-4, blaKPC-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: B1PL86, UniProt: Q9F663*PLUS, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulphate, 5% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.94 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.68 Å / Num. obs: 52930 / % possible obs: 100 % / Redundancy: 12.6 % / Rpim(I) all: 0.074 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2577 / Rpim(I) all: 1.019 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UL8 Resolution: 1.4→45.68 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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