[English] 日本語
Yorodumi- PDB-6y2w: Crystal structure of the single mutant I16K of Low Molecular Weig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y2w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the single mutant I16K of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) | ||||||
Components | Low molecular weight phosphotyrosine protein phosphatase | ||||||
Keywords | HYDROLASE / Engineered | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / sarcolemma / cytoplasmic side of plasma membrane / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Levy, C. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Plos One / Year: 2020 Title: Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme. Authors: Egbe, E. / Levy, C.W. / Tabernero, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y2w.cif.gz | 131 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y2w.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 6y2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/6y2w ftp://data.pdbj.org/pub/pdb/validation_reports/y2/6y2w | HTTPS FTP |
---|
-Related structure data
Related structure data | 6y2vC 1xwwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17886.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P24666, protein-tyrosine-phosphatase, acid phosphatase |
---|---|
#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.28 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris, 25% PEG3350, pH 6.5 Temp details: Cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→33.64 Å / Num. obs: 13623 / % possible obs: 94.05 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.03 / Net I/σ(I): 18.72 |
Reflection shell | Resolution: 1.77→1.833 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 1383 / CC1/2: 0.765 / Rpim(I) all: 0.33 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XWW Resolution: 1.77→33.64 Å / SU ML: 0.2334 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1508
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→33.64 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -17.8958308108 Å / Origin y: -0.924593738142 Å / Origin z: 17.2706834098 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |