+Open data
-Basic information
Entry | Database: PDB / ID: 7q11 | ||||||
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Title | Crystal structure of CTX-M-14 in complex with Ixazomib | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Lactamase / Antibiotic / Resistence | ||||||
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: 1.14 Å | ||||||
Authors | Werner, N. / Perbandt, M. / Hinrichs, W. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Betzel, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as beta-lactamase inhibitors. Authors: Perbandt, M. / Werner, N. / Prester, A. / Rohde, H. / Aepfelbacher, M. / Hinrichs, W. / Betzel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q11.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q11.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 7q11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/7q11 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/7q11 | HTTPS FTP |
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-Related structure data
Related structure data | 7q0yC 7q0zC 6gthS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27888.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase |
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-Non-polymers , 5 types, 404 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-6V8 / [( | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30 % PEG8000, 0.2 M lithium sulfate, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→37.46 Å / Num. obs: 83198 / % possible obs: 99.98 % / Redundancy: 12.4 % / Biso Wilson estimate: 8.08 Å2 / CC1/2: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 29.01 |
Reflection shell | Resolution: 1.14→1.18 Å / Mean I/σ(I) obs: 8.06 / Num. unique obs: 8214 / CC1/2: 0.982 / Rrim(I) all: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GTH Resolution: 1.14→43.59 Å / SU ML: 0.0596 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.7303 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 11.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→43.59 Å
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Refine LS restraints |
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LS refinement shell |
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