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Open data
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Basic information
Entry | Database: PDB / ID: 1es5 | ||||||
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Title | S216A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE | ||||||
![]() | DD-TRANSPEPTIDASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fonze, E. / Charlier, P. | ||||||
![]() | ![]() Title: DD-TRANSPEPTIDASE Authors: Fonze, E. / Rhazi, N. / Nguyen-Disteche, M. / Charlier, P. #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 | ![]() | 64.9 KB | Display | ![]() |
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PDB format | ![]() | 47.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 27492.318 Da / Num. of mol.: 1 / Mutation: S216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39042, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Tris 0.1M, PEG 6K 21 to 30%, NaCl 0.4M, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Details: This particular structure is not described in this paper. |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.38→52.53 Å / Num. obs: 50481 / % possible obs: 93.66 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.6 | ||||||||||||||||||
Reflection shell | Resolution: 1.38→1.44 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.284 / % possible all: 95.2 |
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Processing
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Refinement | Resolution: 1.4→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 11.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
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Xplor file |
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