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- PDB-1kr3: Crystal Structure of the Metallo beta-Lactamase from Bacteroides ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kr3 | ||||||
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Title | Crystal Structure of the Metallo beta-Lactamase from Bacteroides fragilis (CfiA) in Complex with the Tricyclic Inhibitor SB-236050. | ||||||
![]() | beta-Lactamase, type II | ||||||
![]() | HYDROLASE / beta sandwich / protein-inhibitor complex / metallo / beta-lactamase | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. ...Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. / Prez, P. / de la Fuente, J. / Rees, M. / Rivera-Sagredo, A. | ||||||
![]() | ![]() Title: Identification of a series of tricyclic natural products as potent broad-spectrum inhibitors of metallo-beta-lactamases Authors: Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. ...Authors: Payne, D.J. / Hueso-Rodrguez, J.A. / Boyd, H. / Concha, N.O. / Janson, C.A. / Gilpin, M. / Bateson, J.H. / Cheever, C. / Niconovich, N.L. / Pearson, S. / Rittenhouse, S. / Tew, D. / Dez, E. / Prez, P. / de la Fuente, J. / Rees, M. / Rivera-Sagredo, 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 | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 538.9 KB | Display | ![]() |
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Full document | ![]() | 522.9 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hlkC ![]() 1znbS 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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Details | chain A and B do not form a functional dimer |
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Components
#1: Protein | Mass: 25358.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.32 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 32% PEG1000, 0.1M MES, 10microM ZnCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1997 / Details: Ni-filtered |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29 Å / Num. all: 15937 / Num. obs: 15937 / % possible obs: 75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1400 / Rsym value: 0.23 / % possible all: 56 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 10526 / % possible obs: 73.7 % |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.54 Å / % possible obs: 58 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: native CfiA (1ZNB) Resolution: 2.5→29.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 813475.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: MASK / Bsol: 60 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINED MAIN CHAIN ATOMS | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.141 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.22 |