+Open data
-Basic information
Entry | Database: PDB / ID: 1ppn | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF MONOCLINIC PAPAIN AT 1.60 ANGSTROMS RESOLUTION | ||||||
Components | PAPAIN | ||||||
Keywords | HYDROLASE(SULFHYDRYL PROTEINASE) | ||||||
Function / homology | Function and homology information papain / serpin family protein binding / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Carica papaya (papaya) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | ||||||
Authors | Pickersgill, R.W. / Harris, G.W. / Garman, E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Structure of Monoclinic Papain at 1.60 Angstroms Resolution Authors: Pickersgill, R.W. / Harris, G.W. / Garman, E. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: The Segmented Anisotropic Refinement of Monoclinic Papain by the Application of the Rigid-Body Tls Model and Comparison to Bovine Ribonuclease A Authors: Harris, G.W. / Pickersgill, R.W. / Howlin, B. / Moss, D.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ppn.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ppn.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ppn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ppn_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ppn_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 1ppn_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1ppn_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppn ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: ASP 57 - ARG 58 OMEGA =146.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: CIS PROLINE - PRO 152 3: THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED AS AN OXYGEN IN THE REFINEMENT. AN ADDITIONAL OXYGEN ATOM IS PRESENTED AS A HETATM (O) AT THE END OF THE CHAIN. |
-Components
#1: Protein | Mass: 23452.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carica papaya (papaya) / References: UniProt: P00784 |
---|---|
#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-MOH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 5 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / % possible obs: 93 % / Rmerge F obs: 0.0507 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.6→10 Å Details: A SECOND SITE FOR ASN 169 WAS IDENTIFIED AND REFINED, THE OCCUPANCY OF THE TWO SITES REFINED TO 0.47 AND 0.53. THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED ...Details: A SECOND SITE FOR ASN 169 WAS IDENTIFIED AND REFINED, THE OCCUPANCY OF THE TWO SITES REFINED TO 0.47 AND 0.53. THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED AS AN OXYGEN IN THE REFINEMENT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: 'RESTRAINED LEAST-SQUARES' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. reflection obs: 20172 / Rfactor obs: 0.1596 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |