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- PDB-2gfk: Crystal structure of the zinc-beta-lactamase l1 from stenotrophom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gfk | ||||||
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Title | Crystal structure of the zinc-beta-lactamase l1 from stenotrophomonas maltophilia (inhibitor 2) | ||||||
![]() | Metallo-beta-lactamase L1 | ||||||
![]() | HYDROLASE / METALLO / ZN / 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: Journal: Antimicrob.Agents Chemother. / Year: 2004 Title: Update of the standard numbering scheme for class B beta-lactamases Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.M. / Dideberg, O. #2: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fm6C ![]() 2fu7C ![]() 2fu8C ![]() 2fu9C ![]() 2gfjC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#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: PET26 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 454 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/VII.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/VII.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Details
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: 281 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 1.8M ammonium sulfate, 0.1M Hepes pH 7.75, 1.5% V/V Peg 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 31, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.51 Å / Num. obs: 48803 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.357 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SML Resolution: 1.9→19.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.85 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.949 Å / Total num. of bins used: 20
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