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- PDB-1dd6: IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dd6 | ||||||
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Title | IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A MERCAPTOCARBOXYLATE INHIBITOR | ||||||
![]() | IMP-1 METALLO BETA-LACTAMASE | ||||||
![]() | HYDROLASE / METALLO BETA-LACTAMASE INHIBITOR / MERCAPTOCARBOXYLATE INHIBITOR / IMP-1 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 | ![]() ![]() | ||||||
![]() | Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. ...Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S. | ||||||
![]() | ![]() Title: Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor. Authors: Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 549.7 KB | Display | ![]() |
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Full document | ![]() | 562.3 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 25146.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROPS WERE PREPARED BY MIXING EQUAL VOLUMES OF PROTEIN WHICH WAS 14 MG/ ML IN 20MM HEPES, PH 7.5 AND TO WHICH AN EXCESS OF SOLID INHIBITOR HAD BEEN ADDED AND RESERVOIR SOLUTION (30% ...Details: SITTING DROPS WERE PREPARED BY MIXING EQUAL VOLUMES OF PROTEIN WHICH WAS 14 MG/ ML IN 20MM HEPES, PH 7.5 AND TO WHICH AN EXCESS OF SOLID INHIBITOR HAD BEEN ADDED AND RESERVOIR SOLUTION (30% PEG 2000 MONOMETHYLETHER, 0.1M SODIUM ACETATE, PH 5.0 AND 0.2M AMMONIUM SULFATE). THIS MIXTURE WAS INCUBATED OVERNIGHT AT 4C AND CENTRIFUGED TO REMOVE PRECIPITATE BEFORE SETTING UP CRYSTALLIZATION DROPS. CO-CRYSTALS WERE GROWN FROM 6 ML SITTING DROPS OF THE PROTEIN-RESERVOIR SOLUTION AND 0.3 ML OF THE RESERVOIR SOLUTION AT EITHER ROOM TEMPERATURE OR 4C, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Temp details: 293-295 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 35656 / Num. obs: 545270 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 21 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.314 / % possible all: 97.6 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 34187 / % possible obs: 95.9 % / Num. measured all: 545270 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 97.6 % |
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Processing
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Refinement | Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 2 |