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Yorodumi- PDB-1cpy: SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cpy | ||||||
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Title | SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS | ||||||
Components | SERINE CARBOXYPEPTIDASE | ||||||
Keywords | HYDROLASE (CARBOXYPEPTIDASE) | ||||||
Function / homology | Function and homology information phytochelatin biosynthetic process / fungal-type vacuole lumen / carboxypeptidase C / serine-type carboxypeptidase activity / fungal-type vacuole / zymogen activation / macroautophagy / endoplasmic reticulum / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Sorensen, S.B. / Raaschou-Nielsen, M. / Mortensen, U. / Remington, S.J. / Breddam, K. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1995 Title: Site-Directed Mutagenesis on (Serine) Carboxypeptidase Y from Yeast. The Significance of Thr 60 and met 398 in Hydrolysis and Aminolysis Reactions Authors: Sorensen, S.B. / Raaschou-Nielsen, M. / Mortensen, U.H. / Remington, S.J. / Breddam, K. #1: Journal: Biochemistry / Year: 1994 Title: 2.8 Angstroms Structure of Yeast Serine Carboxypeptidase Authors: Endrizzi, J.A. / Breddam, K. / Remington, S.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, 5, 6, 7, 8, 9, 10 AND 11 OF S1A AND S1B ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cpy.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cpy.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 1cpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cpy_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 1cpy_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 1cpy_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1cpy_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/1cpy ftp://data.pdbj.org/pub/pdb/validation_reports/cp/1cpy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 54 / 2: CIS PROLINE - PRO 96 |
-Components
#1: Protein | Mass: 47239.293 Da / Num. of mol.: 1 / Mutation: E65A, E145A / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00729, carboxypeptidase C | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Endrizzi, J.A., (1994) Biochemistry, 33, 11106. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 14110 / % possible obs: 92 % / Observed criterion σ(I): 0 / Num. measured all: 48636 / Rmerge(I) obs: 0.072 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.18 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |