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- PDB-1k25: PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k25 | ||||||
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Title | PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate | ||||||
![]() | low-affinity PENICILLIN-BINDING PROTEIN 2X | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dessen, A. / Mouz, N. / Hopkins, J. / Dideberg, O. | ||||||
![]() | ![]() Title: Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: a mosaic framework containing 83 mutations. Authors: Dessen, A. / Mouz, N. / Gordon, E. / Hopkins, J. / 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 | ![]() | 433.8 KB | Display | ![]() |
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PDB format | ![]() | 339.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 75259.430 Da / Num. of mol.: 4 / Mutation: F364L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.97 % | ||||||||||||||||||||
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: PEG 2000, ammonium sulfate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 15K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→20 Å / Num. all: 52413 / Num. obs: 46531 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 3.2→3.4 Å / Rmerge(I) obs: 0.36 / % possible all: 97.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 167780 |
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.226671 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.392 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.323 |