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Yorodumi- PDB-6q5b: OXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated cefta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q5b | ||||||
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Title | OXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated ceftazidime-avibactam resistance | ||||||
Components | (Beta-lactamase) x 2 | ||||||
Keywords | ANTIBIOTIC / OXA-48 / ceftazidime / avibactam / resistance development / evolution / Escherichia coli / Klebsiella pneumoniae / carbapenemase / carbapenem | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Frohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.K.S. / Samuelsen, O. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Msphere / Year: 2019 Title: OXA-48-Mediated Ceftazidime-Avibactam Resistance Is Associated with Evolutionary Trade-Offs. Authors: Frohlich, C. / Sorum, V. / Thomassen, A.M. / Johnsen, P.J. / Leiros, H.S. / Samuelsen, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q5b.cif.gz | 385.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q5b.ent.gz | 317 KB | Display | PDB format |
PDBx/mmJSON format | 6q5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q5b_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6q5b_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6q5b_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 6q5b_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/6q5b ftp://data.pdbj.org/pub/pdb/validation_reports/q5/6q5b | HTTPS FTP |
-Related structure data
Related structure data | 6q5fC 5qb4S 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 30370.686 Da / Num. of mol.: 2 / Mutation: P68A Source method: isolated from a genetically manipulated source Details: A P68A mutatnt / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506 Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase #2: Protein | Mass: 30413.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bla OXA-48, bla_2, bla_4, blaOXA-48, KPE71T_00045, SAMEA3673128_05462, SAMEA3727643_05844, SAMEA3729690_05506 Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase |
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-Non-polymers , 5 types, 710 molecules
#3: Chemical | ChemComp-NXL / ( #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20 to 30 % polyethylene glycol monomethyl ether 5,000 and 0.1 M bis-tris propane buffer pH 6.5 to 7.5 PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→25 Å / Num. obs: 58434 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2.22 % / CC1/2: 0.994 / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.22→2.28 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5QB4 Resolution: 2.22→24.831 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.03 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→24.831 Å
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Refine LS restraints |
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LS refinement shell |
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