+Open data
-Basic information
Entry | Database: PDB / ID: 1skf | ||||||
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Title | CRYSTAL STRUCTURE OF THE STREPTOMYCES K15 DD-TRANSPEPTIDASE | ||||||
Components | D-ALANYL-D-ALANINE TRANSPEPTIDASE | ||||||
Keywords | PENICILLIN-BINDING / DD-TRANSPEPTIDASE / SERINE PEPTIDASE / BETA-LACTAMASE / HYDROLASE CARBOXYPEPTIDASE | ||||||
Function / homology | Function and homology information 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 | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2 Å | ||||||
Authors | Fonze, E. / Charlier, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15. Authors: Fonze, E. / Vermeire, M. / Nguyen-Disteche, M. / Brasseur, R. / Charlier, P. #1: Journal: J.Mol.Biol. / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1skf.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1skf.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1skf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1skf_validation.pdf.gz | 420.9 KB | Display | wwPDB validaton report |
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Full document | 1skf_full_validation.pdf.gz | 425.3 KB | Display | |
Data in XML | 1skf_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1skf_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/1skf ftp://data.pdbj.org/pub/pdb/validation_reports/sk/1skf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27508.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: K15 References: UniProt: P39042, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→38.4 Å / Num. obs: 23085 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.14 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 38.4 Å / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.099 / Biso Wilson estimate: 17.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 3
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 / Rfactor Rfree: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.266 / Rfactor Rwork: 0.245 |