[English] 日本語
Yorodumi- PDB-5jns: Crystal structure of human low molecular weight protein tyrosine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jns | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with phosphate | ||||||
Components | Low molecular weight phosphotyrosine protein phosphatase | ||||||
Keywords | HYDROLASE / protein tyrosine phosphatase / LMW-PTP / LMPTP | ||||||
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: 1.8 Å | ||||||
Authors | Stanford, S.M. / Aleshin, A.E. / Liddington, R.C. / Bankston, L. / Cadwell, G. / Bottini, N. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase. Authors: Stanford, S.M. / Aleshin, A.E. / Zhang, V. / Ardecky, R.J. / Hedrick, M.P. / Zou, J. / Ganji, S.R. / Bliss, M.R. / Yamamoto, F. / Bobkov, A.A. / Kiselar, J. / Liu, Y. / Cadwell, G.W. / ...Authors: Stanford, S.M. / Aleshin, A.E. / Zhang, V. / Ardecky, R.J. / Hedrick, M.P. / Zou, J. / Ganji, S.R. / Bliss, M.R. / Yamamoto, F. / Bobkov, A.A. / Kiselar, J. / Liu, Y. / Cadwell, G.W. / Khare, S. / Yu, J. / Barquilla, A. / Chung, T.D.Y. / Mustelin, T. / Schenk, S. / Bankston, L.A. / Liddington, R.C. / Pinkerton, A.B. / Bottini, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jns.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jns.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jns ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jns | HTTPS FTP |
---|
-Related structure data
Related structure data | 5jnrSC 5jntC 5jnuC 5jnvC 5jnwC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18209.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACP1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24666, protein-tyrosine-phosphatase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8 / Details: 25% PEG 3350K, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0781 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2015 | |||||||||||||||
Radiation | Monochromator: mirrows / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.74→55.09 Å / Num. obs: 18220 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.1 | |||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JNR Resolution: 1.8→47.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.924 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.62 Å2 / Biso mean: 28.12 Å2 / Biso min: 13.41 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→47.68 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -2.896 Å / Origin y: 4.351 Å / Origin z: -10.601 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|