[English] 日本語
Yorodumi- PDB-2i44: Crystal structure of serine-threonine phosphatase 2C from Toxopla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i44 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of serine-threonine phosphatase 2C from Toxoplasma gondii | ||||||
Components | Serine-threonine phosphatase 2C | ||||||
Keywords | HYDROLASE / phosphatase / PSI-2 / 8817z / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Swamianthan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2007 Title: Structural genomics of protein phosphatases. Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2i44.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2i44.ent.gz | 165.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/2i44 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/2i44 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2iq1C 2irmC 2isnC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36628.191 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WPN9 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.67 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG8000, 0.1M Na Cacodylate, 0.2M Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 66254 / Num. obs: 66254 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Num. unique all: 4428 / % possible all: 61 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.04→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed in remark 465 were not modeled due to lack of electron density. The metal ions are modeled as calcium based on coordination geometry. Further biochemical analysis may be ...Details: Residues listed in remark 465 were not modeled due to lack of electron density. The metal ions are modeled as calcium based on coordination geometry. Further biochemical analysis may be required to confirm the type of metal ion.
| |||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→50 Å
| |||||||||||||||||||||
Refine LS restraints |
|