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- PDB-1ymx: X-ray crystallographic structure of CTX-M-9 beta-lactamase covale... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ymx | |||||||||
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Title | X-ray crystallographic structure of CTX-M-9 beta-lactamase covalently linked to cefoxitin | |||||||||
![]() | beta-lactamase CTX-M-9 | |||||||||
![]() | HYDROLASE / CTX-M / beta-lactamase / acyl-enzyme complex / cefoxitin | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, Y. / Shoichet, B. / Bonnet, R. | |||||||||
![]() | ![]() Title: Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M beta-Lactamases. Authors: Chen, Y. / Shoichet, B. / Bonnet, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 97.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ylyC ![]() 1ylzC ![]() 1ym1C ![]() 1ymsC ![]() 1yljS 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: 27972.494 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: 2.02 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.8 Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2004 / Details: mirrors |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 48520 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.05 / Num. unique all: 4843 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YLJ Resolution: 1.7→19.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 114509.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ONLY 5 ATOMS WERE MODELED FOR A26 THR with the side chain truncated after CB. CFX R2 side chain was missing in the density as well.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2356 Å2 / ksol: 0.400439 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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