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- PDB-2fm6: Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (native form) -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fm6 | ||||||
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Title | Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (native form) | ||||||
![]() | Metallo-beta-lactamase L1 | ||||||
![]() | HYDROLASE / ZN / METALLO / LACTAMASE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nauton, L. / Garau, G. / Kahn, R. / Dideberg, O. | ||||||
![]() | ![]() Title: Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia. Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O. #1: ![]() Title: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O. #2: ![]() Title: A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
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Full document | ![]() | 457.5 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fu7C ![]() 2fu8C ![]() 2fu9C ![]() 2gfjC ![]() 2gfkC ![]() 2h6aC ![]() 2hb9C ![]() 1smlS C: citing same article ( 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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2 | ![]()
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3 | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28740.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: IID 1275 / Cellular location: PERIPLASM / Gene: L1 / Plasmid details: PUB 5832 / Plasmid: PET26 / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979667 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.5 Å / Num. all: 60974 / Num. obs: 64243 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2 / Rsym value: 0.403 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SML Resolution: 1.75→45.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.067 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.221 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.753→1.799 Å / Total num. of bins used: 20 /
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