+Open data
-Basic information
Entry | Database: PDB / ID: 1ysc | |||||||||
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Title | 2.8 ANGSTROMS STRUCTURE OF YEAST SERINE CARBOXYPEPTIDASE | |||||||||
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 / vacuolar lumen / fungal-type vacuole / zymogen activation / cellular response to nitrogen starvation / macroautophagy / endoplasmic reticulum ...phytochelatin biosynthetic process / fungal-type vacuole lumen / carboxypeptidase C / serine-type carboxypeptidase activity / vacuolar lumen / fungal-type vacuole / zymogen activation / cellular response to nitrogen starvation / macroautophagy / endoplasmic reticulum / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | |||||||||
Authors | Endrizzi, J.A. / Remington, S.J. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: 2.8-A 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 | 1ysc.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ysc.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ysc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ysc_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 1ysc_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 1ysc_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1ysc_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/1ysc ftp://data.pdbj.org/pub/pdb/validation_reports/ys/1ysc | 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 3: RESIDUE NAG 871 HAS STRONGER ELECTRON DENSITY BETWEEN IT AND ASN 39 THAN ASN 87. IT IS EXPECTED TO RESIDE ON THE LATTER RESIDUE. |
-Components
#1: Protein | Mass: 47355.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) 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: 2.46 Å3/Da / Density % sol: 49.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 10909 / % possible obs: 93 % / Num. measured all: 46348 / Rmerge(I) obs: 0.043 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.162 / Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection all: 10909 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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