[English] 日本語
Yorodumi- PDB-4nyh: Orthorhombic crystal form of pir1 dual specificity phosphatase core -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nyh | ||||||
---|---|---|---|---|---|---|---|
Title | Orthorhombic crystal form of pir1 dual specificity phosphatase core | ||||||
Components | RNA/RNP complex-1-interacting phosphatase | ||||||
Keywords | HYDROLASE / Dual Specificity Phosphatase / Protein tyrosine Phosphatase / P-loop / Protein Tyrosine Phosphatase (PTP)-fold / RNA-RNP COMPLEX-1 / Dephosphorylation / NUCLEUS | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck ...protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / polynucleotide 5'-phosphatase activity / intercellular bridge / phosphatase activity / RNA processing / protein dephosphorylation / protein tyrosine phosphatase activity / fibrillar center / nuclear speck / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase. Authors: Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nyh.cif.gz | 470.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nyh.ent.gz | 389.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/4nyh ftp://data.pdbj.org/pub/pdb/validation_reports/ny/4nyh | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
|
-Components
#1: Protein | Mass: 21234.215 Da / Num. of mol.: 3 / Fragment: UNP residues 29-205 / Mutation: C152S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP11, PIR1 / Production host: Escherichia coli (E. coli) References: UniProt: O75319, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000, pH 5.5, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||
Detector |
| ||||||||||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||
Reflection | Resolution: 1.2→15 Å / Num. all: 163044 / Num. obs: 163044 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→6 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.477 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 1.059 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.804 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|