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- PDB-6a9t: Crystal structure of Icp55 from Saccharomyces cerevisiae (N-termi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a9t | ||||||
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Title | Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion) | ||||||
![]() | Intermediate cleaving peptidase 55 | ||||||
![]() | HYDROLASE / Intermediate cleaving peptidase 55 / M24B / peptidase / Xaa-Pro aminopeptidase / mitochondrial | ||||||
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 | ![]() ![]() | ||||||
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 | ![]() | 192.4 KB | Display | ![]() |
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PDB format | ![]() | 149.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 703.2 KB | Display | ![]() |
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Full document | ![]() | 704.8 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a9uC ![]() 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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ICP55, YER078C / Plasmid: pST50STR / Details (production host): pET expression palsmid / Production host: ![]() ![]() References: UniProt: P40051, intermediate cleaving peptidase 55 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GLY / | #4: Chemical | ChemComp-JEF / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7 Details: 100 mM HEPES, 30% Jeffamine ED2001, pH 7.0, 0.2 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2014 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→45.35 Å / Num. obs: 31124 / % possible obs: 95.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1901 / CC1/2: 0.69 / Rpim(I) all: 0.357 / Rrim(I) all: 0.92 / % possible all: 68.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A16 Resolution: 2.15→43.727 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→43.727 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.0431 Å / Origin y: -35.1892 Å / Origin z: -15.6558 Å
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Refinement TLS group | Selection details: all |