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Open data
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Basic information
Entry | Database: PDB / ID: 1es3 | ||||||
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Title | C98A mutant of streptomyces K15 DD-transpeptidase | ||||||
![]() | DD-TRANSPEPTIDASE | ||||||
![]() | HYDROLASE / PENICILLIN-BINDING / DD-TRANSPEPTIDASE / SERINE PEPTIDASE / BETA-LACTAMASE / HYDROLASE CARBOXYPEPTIDASE | ||||||
Function / homology | ![]() serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Fonze, E. / Charlier, P. | ||||||
![]() | ![]() Title: Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis. Authors: Rhazi, N. / Charlier, P. / Dehareng, D. / Engher, D. / Vermeire, M. / Frere, J.M. / Nguyen-Disteche, M. / Fonze, E. #1: ![]() Title: The Crystal Structure of a Penicilloyl-Serine Transferase of Intermediate Penicillin Sensitivity Authors: Fonze, E. / Vermeire, M. / Nguyen-Disteche, M. / Brasseur, R. / Charlier, P. #2: ![]() Title: Crystallization and X-Ray Diffraction Study of the Streptomyces K15 Penicillin-Binding Dd-Transpeptidase Authors: Englebert, S. / Charlier, P. / Fonze, E. / To'Th, Y. / Vermeire, M. / Van Beeumen, J. / Grandchamps, J. / Hoffmann, K. / Leyh-Bouille, M. / Nguyen-Disteche, M. / Ghuysen, J.-M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 27476.254 Da / Num. of mol.: 1 / Mutation: C98A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P39042, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.38 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Mes 0.1M, PEG 6K 25%, NaCl 0.5M, pH 6.0, 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: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Jun 24, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.127→42.6 Å / Num. all: 14472 / Num. obs: 14472 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 4.21 |
Reflection shell | Resolution: 2.127→2.203 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.183 / Num. unique all: 730 / % possible all: 46.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 46.8 % / Num. unique obs: 730 |
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Processing
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Refinement | Resolution: 2.2→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 3
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Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.236 |