[English] 日本語
Yorodumi- PDB-2vph: Crystal structure of the human protein tyrosine phosphatase, non-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vph | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ domain | ||||||
Components | TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4 | ||||||
Keywords | HYDROLASE / PROTEIN PHOSPHATASE / PTPN4 / PTPMEG / CYTOSKELETON / MEGAKARYOCYTE / DEPHOSPHORYLATION / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / cytoskeleton / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Roos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Roos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Protein Tyrosine Phosphatase, Non-Receptor Type 4, Pdz Domain Authors: Roos, A.K. / Wang, J. / Burgess-Brown, N. / Elkins, J.M. / Kavanagh, K. / Pike, A.C.W. / Filippakopoulos, P. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Bountra, C. / Knapp, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vph.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vph.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vph ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vph | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
NCS oper: (Code: given Matrix: (0.992, 0.037, -0.117), Vector: |
-Components
#1: Protein | Mass: 11040.697 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 513-606 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-ROSETTA-PRARE2 / References: UniProt: P29074, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 40 % / Description: NONE |
---|---|
Crystal grow | pH: 5 / Details: 20% PEG 3350, 0.20M (NH4)2H(CIT), PH 5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98068 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98068 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 15306 / % possible obs: 100 % / Observed criterion σ(I): 2.8 / Redundancy: 7 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2OCS, 2HE2, 1QAV Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.694 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / 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: 27.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|