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- PDB-1kds: 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: 1kds | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with the inhibitor 3-nitrophenylboronic acid | ||||||
![]() | BETA-LACTAMASE | ||||||
![]() | HYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase / phenylboronic acid inhibitor complex | ||||||
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. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Structure-based approach for binding site identification on AmpC beta-lactamase. Authors: Powers, R.A. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.8 KB | Display | ![]() |
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PDB format | ![]() | 116 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kdwC ![]() 1ke0C ![]() 1ke3C ![]() 1ke4C ![]() 1c3bS 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.74 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate, 590 uM 3-nitrophenylboronic acid, 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: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 24, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 44406 / Num. obs: 43507 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 12.82 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.15→2.25 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.3 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 112903 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 94.7 % / Rmerge(I) obs: 0.222 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1C3B Resolution: 2.15→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.174 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.2431 / Rfactor Rwork: 0.2307 |