+Open data
-Basic information
Entry | Database: PDB / ID: 1es4 | ||||||
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Title | C98N mutant of streptomyces K15 DD-transpeptidase | ||||||
Components | DD-TRANSPEPTIDASE | ||||||
Keywords | HYDROLASE / 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 / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Fonze, E. / Charlier, P. | ||||||
Citation | Journal: Biochemistry / Year: 2003 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: Journal: J.Biol.Chem. / Year: 1999 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: 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 | 1es4.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1es4.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 1es4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es4 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es4 | HTTPS FTP |
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-Related structure data
-Links
-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 |
-Components
#1: Protein | Mass: 27519.279 Da / Num. of mol.: 1 / Mutation: C98N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: K15 / Species (production host): Streptomyces lividans / Production host: Streptomyces lividans TK24 (bacteria) / Strain (production host): TK24 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Tris 0.1M, PEG 6K 30%, NaCl 0.4M, pH 7.2, 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: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→22.69 Å / Num. all: 20385 / Num. obs: 20385 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 8.74 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.182 / Num. unique all: 1634 / % possible all: 95.6 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 95.6 % / Num. unique obs: 1634 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / Rfactor Rfree error: 0.005 / 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: 17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.254 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.238 |