+Open data
-Basic information
Entry | Database: PDB / ID: 1j9m | |||||||||
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Title | K38H 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Fonze, E. / Rhazi, N. / Nguyen-Disteche, M. / 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 | 1j9m.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9m.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j9m_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 1j9m_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 1j9m_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1j9m_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9m ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9m | HTTPS FTP |
-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: 27517.287 Da / Num. of mol.: 1 / Mutation: K38H 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: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#4: 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: 2.33 Å3/Da / Density % sol: 47.12 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Tris 0.1 M, PEG 6K 30%, NaCl 0.4 M, 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→34.71 Å / Num. all: 37427 / Num. obs: 34332 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 19.13 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.139 / % possible all: 39.7 |
Reflection | *PLUS % possible obs: 91.7 % |
Reflection shell | *PLUS % possible obs: 39.7 % / Num. unique obs: 1069 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2 Details: THE ELECTRON DENSITY FOR RESIDUES ILE 145, GLY 146 and ASN 147 IS NOT WELL-DEFINED. THOSE RESIDUES WERE EXCLUDED FROM THE REFINEMENT PROCESS.
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Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.285 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.334 |