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- PDB-2aqv: Crystal Structure of E. coli Isoaspartyl Dipeptidase mutant Y137F -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aqv | ||||||
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Title | Crystal Structure of E. coli Isoaspartyl Dipeptidase mutant Y137F | ||||||
![]() | Isoaspartyl dipeptidase | ||||||
![]() | HYDROLASE / metallo-protease / dipeptidase | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / beta-aspartyl-peptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Marti-Arbona, R. / Thoden, J.B. / Holden, H.M. / Raushel, F.M. | ||||||
![]() | ![]() Title: Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase. Authors: Marti-Arbona, R. / Thoden, J.B. / Holden, H.M. / Raushel, F.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.5 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 463 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aqoC ![]() 1onwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | homo-octomer. Biological assembly is generated by rotation chains A&B around the 4-fold axis located at 1/2,0/z (59.5, 0, 37.55) |
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Components
#1: Protein | Mass: 41151.758 Da / Num. of mol.: 2 / Mutation: Y137F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39377, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG8000, homopipes, madnesium chloride, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 6, 2003 / Details: supper mirrors |
Radiation | Monochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 71537 / Num. obs: 71537 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.065 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.95→2.04 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7448 / Rsym value: 0.264 / % possible all: 81.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1onw Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.224 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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