+Open data
-Basic information
Entry | Database: PDB / ID: 3p09 | ||||||
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Title | Crystal Structure of Beta-Lactamase from Francisella tularensis | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Francisella tularensis subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.898 Å | ||||||
Authors | Kim, Y. / Makowska-Grzyska, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Beta-Lactamase from Francisella tularensis Authors: Kim, Y. / Makowska-Grzyska, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p09.cif.gz | 226.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p09.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 3p09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/3p09 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p09 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32430.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4 / Gene: FTT_0611c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5NH60, beta-lactamase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #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: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 41541 / Num. obs: 41541 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 23.35 Å2 / Rsym value: 0.095 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1728 / Rsym value: 0.671 / % possible all: 83.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.898→40.72 Å / SU ML: 0.22 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.663 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.898→40.72 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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