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Open data
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Basic information
Entry | Database: PDB / ID: 1yal | ||||||
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Title | CARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION | ||||||
![]() | CHYMOPAPAIN | ||||||
![]() | HYDROLASE / THIOL PROTEASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maes, D. / Bouckaert, J. / Poortmans, F. / Wyns, L. / Looze, Y. | ||||||
![]() | ![]() Title: Structure of chymopapain at 1.7 A resolution. Authors: Maes, D. / Bouckaert, J. / Poortmans, F. / Wyns, L. / Looze, Y. #1: ![]() Title: Preparation of Crystals of Chymopapain Diffracting to 1.4 Angstroms Resolution Authors: Azarkan, M. / Maes, D. / Bouckaert, J. / Thi, M.-H.D. / Wyns, L. / Looze, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 42.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.4 KB | Display | ![]() |
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Full document | ![]() | 413.2 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ppoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23777.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE ACTIVE SITE CYS 25 AS WELL AS CYS 117 ARE PROTECTED WITH A THIOMETHYL GROUP Source: (natural) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.88 % | |||||||||||||||
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Crystal grow | pH: 7.6 / Details: pH 7.6 | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 13, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19 Å / Num. obs: 20199 / % possible obs: 84 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.33 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 69 |
Reflection | *PLUS Num. measured all: 39180 |
Reflection shell | *PLUS % possible obs: 68.8 % / Num. unique obs: 2374 / Rmerge(I) obs: 0.222 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PPO Resolution: 1.7→9.5 Å / σ(F): 0
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Displacement parameters | Biso mean: 16.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å / Luzzati d res low obs: 9.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→9.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.79 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |