[English] 日本語
Yorodumi- PDB-4oiw: Structural and kinetic bases for the metal preference of the M18 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oiw | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa | ||||||
Components | Probable M18 family aminopeptidase 2 | ||||||
Keywords | HYDROLASE / Dodecameric TET structure / Aspartyl aminopeptidase / Pseudomonas aeruginosa / Histidine mutation / M18 family | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Nguyen, D.D. / Pandian, R. / Kim, D.D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa Authors: Nguyen, D.D. / Pandian, R. / Kim, D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4oiw.cif.gz | 485.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4oiw.ent.gz | 398.6 KB | Display | PDB format |
PDBx/mmJSON format | 4oiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oiw_validation.pdf.gz | 478.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4oiw_full_validation.pdf.gz | 507.5 KB | Display | |
Data in XML | 4oiw_validation.xml.gz | 92.2 KB | Display | |
Data in CIF | 4oiw_validation.cif.gz | 129.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oiw ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oiw | HTTPS FTP |
-Related structure data
Related structure data | 3wt4C 4njqC 4njrSC 4oidC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46790.480 Da / Num. of mol.: 6 / Mutation: H82A Source method: isolated from a genetically manipulated source Details: 6 histag at the N-terminal / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: apeB, PA3247, Pseudomonas aeruginosa / Plasmid: pVFT1S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: Q9HYZ3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch crystallization / pH: 7.5 Details: 30%(v/v) 2-Propanol, 0.1M Hepes 7.5, 0.2M MgCl2, 10mM Spermidine, 0.1mM ZnCl2, microbatch Crystallization, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.7321 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 24, 2009 |
Radiation | Monochromator: 0.17 2.3 keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7321 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 95594 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.55→2.64 Å / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NJR Resolution: 2.44→48.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.104 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.225 / 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 mean: 39.364 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→48.79 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|