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- PDB-7l91: Structure of Metallo Beta-Lactamase L1 in a Complex with Hydrolyz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l91 | |||||||||
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Title | Structure of Metallo Beta-Lactamase L1 in a Complex with Hydrolyzed Moxalactam Determined by Pink-Beam Serial Crystallography | |||||||||
![]() | Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase) | |||||||||
![]() | HYDROLASE / metallo beta lactamase / moxalactam / serial crystallography / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Henning, R. / Maltseva, N. / Endres, M. / Babnigg, G. / Vukica, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase. Authors: Wilamowski, M. / Sherrell, D.A. / Kim, Y. / Lavens, A. / Henning, R.W. / Lazarski, K. / Shigemoto, A. / Endres, M. / Maltseva, N. / Babnigg, G. / Burdette, S.C. / Srajer, V. / Joachimiak, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 89.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7uhhC ![]() 7uhiC ![]() 7uhjC ![]() 7uhkC ![]() 7uhlC ![]() 7uhmC ![]() 7uhnC ![]() 7uhoC ![]() 7uhpC ![]() 7uhqC ![]() 7uhrC ![]() 7uhsC ![]() 7uhtC ![]() 7l52S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 29243.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-XQP / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 289 K / Method: batch mode Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate ...Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Feb 11, 2020 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→33.03 Å / Num. obs: 14754 / % possible obs: 86.42 % / Redundancy: 35.4 % / Biso Wilson estimate: 22.15 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 30.51 | |||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 15.96 / Num. unique obs: 1143 | |||||||||
Serial crystallography sample delivery | Description: Nylon Mesh / Method: fixed target | |||||||||
Serial crystallography sample delivery fixed target | Description: ALEX mesh holder Motion control: SmarAct Motors viaPMAC start/stop raster over area Sample holding: nylon mesh Sample solvent: buffer 0.0075 Tris, 0.05 M KCl, 0.75 mM TCEP, 2.5 mM ZnCl2, 0.075 M sodium malonate pH 8.0, 10% (w/v) PEG3350 Support base: xyz stage | |||||||||
Serial crystallography data reduction | Crystal hits: 7816 / Frames indexed: 583 / Frames total: 19316 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7L52 Resolution: 2.2→33.03 Å / SU ML: 0.2118 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.7205 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: 26.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.03 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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