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Yorodumi- PDB-2dea: Crystal Structure of the Aminopeptidase of Aeromonas proteolytica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dea | ||||||
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Title | Crystal Structure of the Aminopeptidase of Aeromonas proteolytica at pH 4.7 | ||||||
Components | Bacterial leucyl aminopeptidase | ||||||
Keywords | HYDROLASE / aminopeptidase / metalloenzyme / bimetalloenzyme / low pH / zinc enzyme | ||||||
Function / homology | Function and homology information bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio proteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.24 Å | ||||||
Authors | Petsko, G.A. / Ringe, D. / Desmarais, W. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2006 Title: The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica. Authors: Desmarais, W. / Bienvenue, D.L. / Bzymek, K.P. / Petsko, G.A. / Ringe, D. / Holz, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dea.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dea.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 2dea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/2dea ftp://data.pdbj.org/pub/pdb/validation_reports/de/2dea | 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32238.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q01693, bacterial leucyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #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: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: NaAcetate, KSCN, NaCl, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2001 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→30 Å / Num. obs: 81189 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Highest resolution: 1.24 Å / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.24→30 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.24→30 Å
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