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- PDB-8b3m: Millisecond cryo-trapping by the spitrobot crystal plunger, CTXM-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b3m | ||||||
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Title | Millisecond cryo-trapping by the spitrobot crystal plunger, CTXM-14 Avibactam complex, SSX, 1 sec | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / beta-lactamase / CTX-M-14 / time-resolved crystallography | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.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 | ![]() | 148.2 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.4 KB | Display | ![]() |
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Full document | ![]() | 838.2 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aw8C ![]() 8aw9C ![]() 8awbC ![]() 8awcC ![]() 8awdC ![]() 8aweC ![]() 8awfC ![]() 8awsC ![]() 8awuC ![]() 8awvC ![]() 8awxC ![]() 8awyC ![]() 8b03C ![]() 8b05C ![]() 8b06C ![]() 8b08C ![]() 8b2oC ![]() 8b2vC ![]() 8b2wC ![]() 6gthS S: Starting model for refinement 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 27658.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NXL / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4.5 / Details: 40% PEG8000, 200 mM LiSO4, 100 mM NaOAc, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→77.62 Å / Num. obs: 18275 / % possible obs: 100 % / Redundancy: 532.7 % / Biso Wilson estimate: 21.53 Å2 / CC1/2: 0.9637 / CC star: 0.9907 / Net I/σ(I): 6.37 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 369 % / Num. unique obs: 1175284 / CC1/2: 0.73 / CC star: 0.9186 / % possible all: 100 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6gth Resolution: 1.97→77.62 Å / SU ML: 0.2825 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.669 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: 28.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→77.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.00138942196 Å / Origin y: 3.81404587362 Å / Origin z: -19.1152137962 Å
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Refinement TLS group | Selection details: all |