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- PDB-1i5q: CRYSTAL STRUCTURE OF THE E. COLI AMPC BETA-LACTAMASE MUTANT N152A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i5q | ||||||
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Title | CRYSTAL STRUCTURE OF THE E. COLI AMPC BETA-LACTAMASE MUTANT N152A COVALENTLY ACYLATED WITH THE INHIBITORY BETA-LACTAM, MOXALACTAM | ||||||
![]() | BETA-LACTAMASE | ||||||
![]() | HYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trehan, I. / Beadle, B.M. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site. Authors: Trehan, I. / Beadle, B.M. / 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 | ![]() | 158 KB | Display | ![]() |
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PDB format | ![]() | 124.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c3bS 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: 39544.898 Da / Num. of mol.: 2 / Mutation: N152A 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: 50.9 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate, AmpC N152A, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Temperature: 23 ℃ |
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: Aug 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→20 Å / Num. all: 68795 / Num. obs: 274720 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 21.732 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.08 |
Reflection shell | Resolution: 1.83→1.87 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.69 / Num. unique all: 4551 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 68795 / Num. measured all: 274720 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1C3B with inhibitor, solvent, and N152 sidechain atoms (beyond C-beta) removed Resolution: 1.83→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.83→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.87 Å / Total num. of bins used: 15 /
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Xplor file | Serial no: 1 / Param file: moxalactam.par / Topol file: moxalactam.top | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 3 % / Rfactor obs: 0.168 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0139 |