[English] 日本語
Yorodumi- PDB-3jtq: Mutations in Cephalosporin Acylase Affecting Stability and Autopr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jtq | ||||||
---|---|---|---|---|---|---|---|
Title | Mutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis | ||||||
Components | (Glutaryl 7-aminocephalosporanic acid acylase) x 2 | ||||||
Keywords | HYDROLASE / cephalosporin acylase / Autoproteolysis | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Structural features of cephalosporin acylase reveal the basis of autocatalytic activation. Authors: Cho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3jtq.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3jtq.ent.gz | 225.2 KB | Display | PDB format |
PDBx/mmJSON format | 3jtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/3jtq ftp://data.pdbj.org/pub/pdb/validation_reports/jt/3jtq | HTTPS FTP |
---|
-Related structure data
Related structure data | 3jtrC 2advS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18506.191 Da / Num. of mol.: 1 / Fragment: UNP residues 30-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 59169.777 Da / Num. of mol.: 1 / Fragment: UNP residues 199-720 / Mutation: L210N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.51 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Na-cacodylate (pH 6.5), 0.2M magnesium chloride, PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 55819 / Num. obs: 53754 / % possible obs: 96.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 5 / % possible all: 90.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ADV Resolution: 2.2→48.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.959 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.19 Å2 / Biso mean: 34.323 Å2 / Biso min: 15.81 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.39 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.198→2.255 Å / Total num. of bins used: 20
|