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- PDB-6a9u: Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a9u | |||||||||
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Title | Crystal strcture of Icp55 from Saccharomyces cerevisiae bound to apstatin inhibitor | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Intermediate cleaving peptidase 55 / M24B / peptidase / Xaa-Pro aminopeptidase / mitochondrial / Apstatin / N-((2S / 3R)-3-Amino-2-hydroxy-4-phenylbutanoyl)-Pro-Pro-Ala-NH2 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() intermediate cleaving peptidase 55 / metalloaminopeptidase activity / aminopeptidase activity / protein processing / manganese ion binding / mitochondrial inner membrane / protein stabilization / mitochondrion / proteolysis / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singh, R. / Kumar, A. / Goyal, V.D. / Makde, R.D. | |||||||||
![]() | ![]() Title: Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function. Authors: Singh, R. / Goyal, V.D. / Kumar, A. / Sabharwal, N.S. / Makde, R.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.6 KB | Display | ![]() |
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PDB format | ![]() | 142.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a9tC ![]() 6a9vC ![]() 1a16S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 51358.691 Da / Num. of mol.: 1 / Mutation: D189E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P40051, intermediate cleaving peptidase 55 | ||
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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: 3.29 Å3/Da / Density % sol: 62.61 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 Details: 100mM hipis pH 7 , 28% Jagffamine ED 2003 pH7, 2mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.76 Å / Num. obs: 27387 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2843 / CC1/2: 0.71 / Rpim(I) all: 0.487 / Rrim(I) all: 0.903 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A16 Resolution: 2.4→47.758 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.758 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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