+Open data
-Basic information
Entry | Database: PDB / ID: 2hc2 | ||||||
---|---|---|---|---|---|---|---|
Title | Engineered protein tyrosine phosphatase beta catalytic domain | ||||||
Components | Receptor-type tyrosine-protein phosphatase beta | ||||||
Keywords | HYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design | ||||||
Function / homology | Function and homology information glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery. Authors: Evdokimov, A.G. / Pokross, M. / Walter, R. / Mekel, M. / Cox, B. / Li, C. / Bechard, R. / Genbauffe, F. / Andrews, R. / Diven, C. / Howard, B. / Rastogi, V. / Gray, J. / Maier, M. / Peters, K.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hc2.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hc2.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hc2_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2hc2_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 2hc2_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2hc2_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/2hc2 ftp://data.pdbj.org/pub/pdb/validation_reports/hc/2hc2 | HTTPS FTP |
-Related structure data
Related structure data | 2hc1SC 2i3rC 2i3uC 2i4eC 2i4gC 2i4hC 2i5xC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33780.340 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB / Plasmid: pHisMBP-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P23467, protein-tyrosine-phosphatase | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#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 Å3/Da / Density % sol: 38.44 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.85 Details: 21% PEG 8000, 200 mM MgCl2, 1% BME, 0.1% BOG, 1mM DTT, 80 mM Na Citrate, pH 7.85, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
---|---|
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 2, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→33.67 Å / Num. all: 48397 / Num. obs: 48397 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.87 / % possible all: 69.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HC1 Resolution: 1.4→33.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.945 / SU ML: 0.035 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.065 / 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: 19.055 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→33.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|