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Yorodumi- PDB-6a9t: Crystal structure of Icp55 from Saccharomyces cerevisiae (N-termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a9t | ||||||
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Title | Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion) | ||||||
Components | Intermediate cleaving peptidase 55 | ||||||
Keywords | HYDROLASE / Intermediate cleaving peptidase 55 / M24B / peptidase / Xaa-Pro aminopeptidase / mitochondrial | ||||||
Function / homology | Function and homology information intermediate cleaving peptidase 55 / metalloaminopeptidase activity / aminopeptidase activity / protein processing / manganese ion binding / protein stabilization / mitochondrial inner membrane / mitochondrion / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Singh, R. / Kumar, A. / Goyal, V.D. / Makde, R.D. | ||||||
Citation | Journal: FEBS Lett. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a9t.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a9t.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 6a9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a9t_validation.pdf.gz | 703.2 KB | Display | wwPDB validaton report |
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Full document | 6a9t_full_validation.pdf.gz | 704.8 KB | Display | |
Data in XML | 6a9t_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 6a9t_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/6a9t ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a9t | HTTPS FTP |
-Related structure data
Related structure data | 6a9uC 6a9vC 1a16S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 51358.691 Da / Num. of mol.: 1 / Mutation: D189E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ICP55, YER078C / Plasmid: pST50STR / Details (production host): pET expression palsmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |