+Open data
-Basic information
Entry | Database: PDB / ID: 3qcb | ||||||
---|---|---|---|---|---|---|---|
Title | Human receptor protein tyrosine phosphatase gamma, domain 1, apo | ||||||
Components | Receptor-type tyrosine-protein phosphatase gamma | ||||||
Keywords | HYDROLASE / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / APO | ||||||
Function / homology | Function and homology information negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of neuron projection development / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W. #1: Journal: To be Published Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qcb.cif.gz | 130 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qcb.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/3qcb ftp://data.pdbj.org/pub/pdb/validation_reports/qc/3qcb | HTTPS FTP |
---|
-Related structure data
Related structure data | 3qccC 3qcdC 3qceC 3qcfC 3qcgC 3qchC 3qciC 3qcjC 3qckC 3qclC 3qcmC 3qcnC 1rpmS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35707.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPG, PTPRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.37 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 6.5 / Details: pH 6.5, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 15, 2005 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 43827 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPM WITH LOOPS EXCISED AND NON- IDENTICAL SIDE CHAINS SHORN. Resolution: 2.1→23.66 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 2223360 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.64 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→23.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|