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- PDB-1y0y: Crystal structure of tetrahedral aminopeptidase from P. horikoshi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y0y | |||||||||
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Title | Crystal structure of tetrahedral aminopeptidase from P. horikoshii in complex with amastatin | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / aminopeptidase / PDZ / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Groll, M. / Borissenko, L. | |||||||||
![]() | ![]() Title: Crystal Structure of TET Protease Reveals Complementary Protein Degradation Pathways in Prokaryotes Authors: Borissenko, L. / Groll, 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 | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 446 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | The biological assembly is generated: x,y,z; x,-y,-z; -x,y,-z; -x,-y,z; z,x,y; -z,-x,y; z,-x,-y; -z,x,-y; y,z,x; -y,z,-x; -y,-z,x; y,-z,-x |
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Components
#1: Protein | Mass: 39071.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 21, 2004 |
Radiation | Monochromator: Si(111) double crystal, non dispersive / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. obs: 60465 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.448 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.5803 Å2 / ksol: 0.360596 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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