[English] 日本語
![](img/lk-miru.gif)
- PDB-2i42: Crystal structure of Yersinia protein tyrosine phosphatase comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2i42 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue | ||||||
![]() | Tyrosine-protein phosphatase | ||||||
![]() | HYDROLASE / Yersinia PTPase / vanadate / transition state analogue | ||||||
Function / homology | ![]() dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vijayalakshmi, J. / Saper, M.A. | ||||||
![]() | ![]() Title: Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue Authors: Vijayalakshmi, J. / Saper, M.A. #1: Journal: PROC.NATL.ACAD.SCI.USA / Year: 1995 Title: Visualization of intermediate and transition-state structures in protein tyrosine phosphatase catalysis. Authors: Denu, J.M. / Lohse, D.L. / Vijayalakshmi, J. / Saper, M.A. / Dixon, J.E. #2: ![]() Title: A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase. Authors: Schubert, H.L. / Fauman, E.B. / Stuckey, J.A. / Dixon, J.E. / Saper, M.A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Dissecting the catalytic mechanism of protein tyrosine phosphatases. Authors: Zhang, Z.-Y. / Wang, Y. / Dixon, J.E. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED ...HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED TO SG ATOM OF CYS 403 WITH A BONDING DISTANCE OF 2.52 A. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.1 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: Tyrosine-protein phosphatase / Mutation: C235R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-VO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 41.25 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 400 mM NaCl, 14% PEG 4K, 5% 2-proponol .15% BME, 100mM Tris HCl pH 8.5, 1mM vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→10 Å / Num. all: 13593 / Num. obs: 13593 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4.02 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.1→2.3 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.25 / Num. unique all: 1336 / % possible all: 74.3 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entries 1YTW and 1YTS Resolution: 2.2→7 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Residues Met163-Val186 were not included in the refinement due to missing electron densities.
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2 | ||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å
|