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Open data
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Basic information
Entry | Database: PDB / ID: 1dy6 | ||||||
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Title | Structure of the imipenem-hydrolyzing beta-lactamase SME-1 | ||||||
![]() | CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1 | ||||||
![]() | HYDROLASE / LACTAMASE / ANTIBIOTIC / CARBAPENEM / IMIPENEM | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sougakoff, W. / L'Hermite, G. / Billy, I. / Guillet, V. / Naas, T. / Nordman, P. / Jarlier, V. / Delettre, J. | ||||||
![]() | ![]() Title: Structure of the Imipenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens. Authors: Sougakoff, W. / L'Hermite, G. / Billy, I. / Pernot, L. / Guillet, V. / Naas, T. / Nordmann, P. / Jarlier, V. / Delettre, J. #1: Journal: J.Struct.Biol. / Year: 1996 Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Analysis of the Carbapenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens Authors: Sougakoff, W. / Jarlier, V. / Delettre, J. / Colloc'H, N. / L'Hermite, G. / Nordmann, P. / Naas, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.4 KB | Display | ![]() |
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PDB format | ![]() | 93.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.8 KB | Display | ![]() |
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Full document | ![]() | 376.1 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bueS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.986365, 0.004914, 0.164497), Vector: Details | BIOLOGICAL UNIT: MONOMER | |
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Components
#1: Protein | Mass: 29386.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: APO FORM / Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | SEQUENCE DESCRIBED IN NAAS T., VANDEL L., SOUGAKOFF W., LIVERMORE D.M., NORDMANN P. ANTIMICROB. ...SEQUENCE DESCRIBED IN NAAS T., VANDEL L., SOUGAKOFF W., LIVERMORE D.M., NORDMANN P. ANTIMICROB | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 17% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL, PH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. obs: 24447 / % possible obs: 82 % / Redundancy: 2.3 % / Rsym value: 0.049 |
Reflection | *PLUS % possible obs: 82 % / Num. measured all: 55772 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Highest resolution: 2.13 Å / Lowest resolution: 2.28 Å / % possible obs: 30.1 % / Redundancy: 2.1 % / Num. unique obs: 1601 / Num. measured obs: 3390 / Rmerge(I) obs: 0.216 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: MODIFIED NMC-A BETA-LACTAMASE (1BUE) SOFTWARE USED: AMORE Resolution: 2.13→10 Å / Rfactor Rfree error: 0.005 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: A FLAT TWO-LOBE ELECTRON DENSITY IS LOCATED IN A AND IN B BETWEEN SER130, THR235 AND SER237. IT HAS BEEN ASSOCIATED WITH A MODEL OF TWO WATER MOLECULES, 111 AND 186 IN MOLECULE A AND 89 AND 143 IN MOLECULE B.
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Displacement parameters | Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→10 Å
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Refine LS restraints |
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