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- PDB-8pcm: Structure of serine-beta-lactamase CTX-M-14 following the time-re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8pcm | ||||||||||||
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Title | Structure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid and subsequent glycerol-boric acid-ester formation, 80 ms | ||||||||||||
![]() | Beta-lactamase | ||||||||||||
![]() | HYDROLASE / catalytic activity / beta-lactamase activity / hydrolase activity / inhibitor / time-resolved / tape drive | ||||||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Prester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Yefanov, O. / Hinrichs, W. / Rohde, H. / Betzel, C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Time resolved crystallography of boric acid binding to the active site serine of the beta-lactamase CTX-M-14 and subsequent 1,2-diol esterification Authors: Prester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Werner, N. / Henkel, A. / Maracke, J. / Yefanov, O. / Hakanpaeae, J. / Pompidor, G. / Meyer, J. / Chapman, H. / Aepfelbacher, M. ...Authors: Prester, A. / Perbandt, M. / Galchenkova, M. / Oberthuer, D. / Werner, N. / Henkel, A. / Maracke, J. / Yefanov, O. / Hakanpaeae, J. / Pompidor, G. / Meyer, J. / Chapman, H. / Aepfelbacher, M. / Hinrichs, W. / Rohde, H. / Betzel, C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 131.5 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 | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pc9C ![]() 8pcaC ![]() 8pcbC ![]() 8pccC ![]() 8pcdC ![]() 8pceC ![]() 8pcfC ![]() 8pcgC ![]() 8pciC ![]() 8pcjC ![]() 8pckC ![]() 8pclC ![]() 8pcnC ![]() 8pcoC ![]() 8pcpC ![]() 8pcqC ![]() 8pcrC ![]() 8pcsC ![]() 8pctC ![]() 8pcuC ![]() 8pcvC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28000.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-YCH / [( |
#3: Chemical | ChemComp-BO4 / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 50% CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch crystallization setups |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→38.88 Å / Num. obs: 21824 / % possible obs: 100 % / Redundancy: 3113 % / Biso Wilson estimate: 38.76 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 10.73 |
Reflection shell | Resolution: 1.84→1.86 Å / Num. unique obs: 1402 / CC1/2: 0.195 / CC star: 0.572 |
Serial crystallography sample delivery | Description: CFEL TapeDrive / Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→38.88 Å
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Refine LS restraints |
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LS refinement shell |
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