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Yorodumi- PDB-5jnu: Crystal structure of mouse Low-Molecular Weight Protein Tyrosine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jnu | ||||||
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Title | Crystal structure of mouse Low-Molecular Weight Protein Tyrosine Phosphatase type A (LMPTP-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 / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / sarcolemma / SH3 domain binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.535 Å | ||||||
Authors | Stanford, S.M. / Aleshin, A.E. / Liddington, R.C. / Bankston, L. / Cadwell, G. / Bottini, N. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jnu.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jnu.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 5jnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jnu_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 5jnu_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 5jnu_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5jnu_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jnu ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jnu | HTTPS FTP |
-Related structure data
Related structure data | 5jnrSC 5jnsC 5jntC 5jnvC 5jnwC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18359.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acp1 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9D358, protein-tyrosine-phosphatase #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.19 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 7% PEG 10K, Bis Tris, Ammonium Acetate; soaked in NaPO4 buffer before data collection |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2015 | |||||||||||||||
Radiation | Monochromator: mirrows / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.53→38.58 Å / Num. obs: 9354 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.074 / Rrim(I) all: 0.157 / Net I/σ(I): 6.7 / Num. measured all: 40453 / Scaling rejects: 76 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JNR Resolution: 2.535→38.576 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.6 Å2 / Biso mean: 43.9639 Å2 / Biso min: 21.97 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.535→38.576 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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