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- PDB-1rcj: Crystal structure of E166A mutant of SHV-1 beta-lactamase with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rcj | ||||||
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Title | Crystal structure of E166A mutant of SHV-1 beta-lactamase with the trans-enamine intermediate of tazobactam | ||||||
![]() | Beta-lactamase SHV-1 | ||||||
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Function / homology | ![]() beta-lactam antibiotic catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Hujer, A.M. / Carey, P.R. / Bonomo, R.A. / van den Akker, F. | ||||||
![]() | ![]() Title: Tazobactam Forms a Stoichiometric trans-Enamine Intermediate in the E166A Variant of SHV-1 beta-Lactamase: 1.63 A Crystal Structure Authors: Padayatti, P.S. / Helfand, M.S. / Totir, M.A. / Carey, M.P. / Hujer, A.M. / Carey, P.R. / Bonomo, R.A. / Van Den Akker, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1g56 S: Starting model for refinement |
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Similar structure data |
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Links
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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 / Mutation: E166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P14557, UniProt: P0AD64*PLUS, ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-TBI / | #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystal was soaked for 20 minutes in mother liquor containing 5mM Tazobactam prior to flash freezing. 30% PEG 6000, 0.1M HEPES, 0.56mM Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2003 / Details: Yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.63→30 Å / Num. all: 29632 / Num. obs: 28328 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.032 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 1.63→1.69 Å / Rsym value: 0.08 / % possible all: 87.7 |
Reflection | *PLUS Rmerge(I) obs: 0.032 |
Reflection shell | *PLUS % possible obs: 87.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 12.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1G56 ![]() 1g56 Resolution: 1.63→30 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.63→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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