+Open data
-Basic information
Entry | Database: PDB / ID: 1es5 | ||||||
---|---|---|---|---|---|---|---|
Title | S216A 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: 1.4 Å | ||||||
Authors | Fonze, E. / Charlier, P. | ||||||
Citation | Journal: To be Published Title: DD-TRANSPEPTIDASE Authors: Fonze, E. / Rhazi, N. / Nguyen-Disteche, M. / Charlier, P. #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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1es5.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1es5.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1es5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1es5_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1es5_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 1es5_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1es5_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es5 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 27492.318 Da / Num. of mol.: 1 / Mutation: S216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: K15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P39042, serine-type D-Ala-D-Ala carboxypeptidase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
---|---|
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 |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|