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- PDB-1l2s: X-ray crystal structure of AmpC beta-lactamase from E. coli in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l2s | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a DOCK-predicted non-covalent inhibitor | ||||||
![]() | beta-lactamase | ||||||
![]() | HYDROLASE / beta-lactamase-inhibitor complex / cephalosporinase | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Powers, R.A. / Morandi, F. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Authors: Powers, R.A. / Morandi, F. / Shoichet, B.K. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). IN SOLUTION, AMPC IS BELIEVED TO BE FUNCTIONAL IN ITS MONOMERIC FORM. | ||||||
Remark 600 | HETEROGEN THE CONFORMATION OF THE LIGAND STC WAS DETERMINED EXPERIMENTALLY. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.4 KB | Display | ![]() |
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PDB format | ![]() | 121.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ke4S 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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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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate, 1.2 mM inhibitor (STC), pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Details: used microseeding | ||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Dec 19, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→20 Å / Num. obs: 56580 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.21 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.94→1.99 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 4.2 / % possible all: 95.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 208148 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 95.1 % / Rmerge(I) obs: 0.315 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1KE4 Resolution: 1.94→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Electron density for residues 290-292 of chain A was poor, and are not present in the final model.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.03 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.173 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2296 / Rfactor Rwork: 0.1917 |