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- PDB-1ll9: Crystal Structure Of AmpC beta-Lactamase From E. Coli In Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ll9 | ||||||
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Title | Crystal Structure Of AmpC beta-Lactamase From E. Coli In Complex With Amoxicillin | ||||||
![]() | beta-lactamase![]() | ||||||
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Function / homology | ![]() antibiotic catabolic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trehan, I. / Morandi, F. / Blaszczak, L.C. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Using steric hindrance to design new inhibitors of class C beta-lactamases. Authors: Trehan, I. / Morandi, F. / Blaszczak, L.C. / Shoichet, B.K. | ||||||
History |
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Remark 600 | heterogen The het group AXL was origianlly amoxicillin before the compound underwent a nucleophilic ...heterogen The het group AXL was origianlly amoxicillin before the compound underwent a nucleophilic attack at the C1 by the Ser64 residue and is now covalently bound to Ser64. This attack breaks the bond between C1 and N7, thus opening the 4-membered ring. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1llbC ![]() 1ke4S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-AXL / | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate, AmpC, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Temperature: 23 ℃ / Details: Trehan, I., (2001) Biochemistry, 40, 7992. |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 5, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.87→20 Å / Num. all: 63012 / Num. obs: 63012 / % possible obs: 97 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.056 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.87→1.91 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.92 / % possible all: 97 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 225850 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.373 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1KE4 with solvent atoms removed Resolution: 1.87→20 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.87→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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