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Yorodumi- PDB-2isn: Crystal structure of a phosphatase from a pathogenic strain Toxop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2isn | ||||||
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Title | Crystal structure of a phosphatase from a pathogenic strain Toxoplasma gondii | ||||||
Components | NYSGXRC-8828z, phosphatase | ||||||
Keywords | HYDROLASE / 8828z / phosphatase / pathogenic strain / praseodymium / sulfate / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 4-Layer Sandwich / Alpha Beta / PRASEODYMIUM ION Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2isn.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2isn.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 2isn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2isn ftp://data.pdbj.org/pub/pdb/validation_reports/is/2isn | HTTPS FTP |
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-Related structure data
Related structure data | 1rxdC 2fh7C 2g59C 2hcmC 2hhlC 2hxpC 2hy3C 2i0oC 2i1yC 2i44C 2iq1C 2irmC 2nv5C 2oycC 2p27C 2p4uC 2p69C 2p8eC 2pbnC 2q5eC 2qjcC 2r0bC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40230.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pSGX4(BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 2M Li2So4, 0.5M Ammonium sulfate, 0.1M Na-citrate, ph 5.6, praseodymium acetate, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 54775 / Num. obs: 54775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1 / Num. unique all: 5424 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: none Resolution: 1.9→43.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 68658.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: the missing residues listed in Remark 465 are due to lack of electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.6401 Å2 / ksol: 0.35205 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 13.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→43.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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