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Yorodumi- PDB-4mbh: Penam sulfone PSR-3-226 bound to E166A variant of SHV-1 beta-lactamase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mbh | ||||||
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Title | Penam sulfone PSR-3-226 bound to E166A variant of SHV-1 beta-lactamase | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / Class A 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 / FOURIER SYNTHESIS / Resolution: 1.22 Å | ||||||
Authors | Rodkey, E.A. / van den Akker, F. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Penam sulfones and beta-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition. Authors: Rodkey, E.A. / Winkler, M.L. / Bethel, C.R. / Pagadala, S.R. / Buynak, J.D. / Bonomo, R.A. / van den Akker, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mbh.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mbh.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/4mbh ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mbh | HTTPS FTP |
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-Related 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: 28848.982 Da / Num. of mol.: 1 / Fragment: SHV-1 beta-lactamase / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AD64, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-0RJ / | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 21-30% PEG 6000, 0.1M HEPES. 0.56mM Cymal-6, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 6.8-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 27, 2010 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→24.34 Å / Num. all: 65934 / Num. obs: 65684 / % possible obs: 99.62 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.218→1.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 6.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.22→24.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.918 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.299 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→24.34 Å
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Refine LS restraints |
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