[English] 日本語
![](img/lk-miru.gif)
- PDB-2jet: Crystal structure of a trypsin-like mutant (S189D , A226G) chymot... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2jet | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a trypsin-like mutant (S189D , A226G) chymotrypsin. | ||||||
![]() |
| ||||||
![]() | HYDROLASE / SUBSTRATE SPECIFICITY / ZYMOGEN / PROTEASE / DIGESTION / SERINE PROTEASE / PROTEIN ENGINEERING | ||||||
Function / homology | ![]() Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to toxic substance / response to peptide hormone ...Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to toxic substance / response to peptide hormone / peptidase activity / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jelinek, B. / Katona, G. / Fodor, K. / Venekei, I. / Graf, L. | ||||||
![]() | ![]() Title: The Crystal Structure of a Trypsin-Like Mutant Chymotrypsin: The Role of Position 226 in the Activity and Specificity of S189D Chymotrypsin. Authors: Jelinek, B. / Katona, G. / Fodor, K. / Venekei, I. / Graf, L. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kdqS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 1544.833 Da / Num. of mol.: 1 / Fragment: RESIDES 19-28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein | Mass: 13880.524 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Protein | Mass: 10253.702 Da / Num. of mol.: 1 / Fragment: RESIDUES 165-263 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | FIRST FIVE RESIDUE ARE DUE TO THE EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.8 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: VAPOR DIFFUSION METHOD, 0.1M HEPES, PH 7.0, 30% PEG6000 AND PROTEIN (15 MG/ML) WITH BENZAMIDINE TWOFOLD EXCESS MIXED 1:1, 20 C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2005 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→64.42 Å / Num. obs: 9753 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 95.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KDQ Resolution: 2.2→43.23 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.834 / SU B: 24.796 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDECHAINS WITH 0 OCCUPANCY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|