+Open data
-Basic information
Entry | Database: PDB / ID: 1i2s | ||||||
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Title | BETA-LACTAMASE FROM BACILLUS LICHENIFORMIS BS3 | ||||||
Components | BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / serine beta-lactamase / antibiotic resistance | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fonze, E. / Vanhove, M. / Dive, G. / Sauvage, E. / Frere, J.M. / Charlier, P. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structures of the Bacillus licheniformis BS3 class A beta-lactamase and of the acyl-enzyme adduct formed with cefoxitin Authors: Fonze, E. / Vanhove, M. / Dive, G. / Sauvage, E. / Frere, J.M. / Charlier, P. #1: Journal: FEBS Lett. / Year: 1997 Title: Unexpected influence of a C-terminal-fused His-tag on the processing of an enzyme and on the kinetic and folding parameters Authors: Ledent, P. / Duez, C. / Vanhove, M. / Lejeune, A. / Fonze, E. / Charlier, P. / Rhazi-Filali, F. / Thamm, I. / Guillaume, G. / Samyn, B. / Devreese, B. / Van Beeumen, J. / Lamotte-Brasseur, J. / Frere, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i2s.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i2s.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i2s_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 1i2s_full_validation.pdf.gz | 475.5 KB | Display | |
Data in XML | 1i2s_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1i2s_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/1i2s ftp://data.pdbj.org/pub/pdb/validation_reports/i2/1i2s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 31286.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Plasmid: P-ET-22(B)KR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00808, beta-lactamase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.22 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 1.653→23.74 Å / Num. all: 70471 / Num. obs: 70471 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.653→1.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.9 / % possible all: 79.1 |
Reflection | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 23.74 Å / Num. measured all: 165623 |
Reflection shell | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 1.97 Å / % possible obs: 89.7 % / Num. possible: 27770 / Num. measured obs: 64168 / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor Rfree: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.362 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.351 |