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Yorodumi- PDB-3jvi: Product state mimic crystal structure of protein tyrosine phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jvi | ||||||
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Title | Product state mimic crystal structure of protein tyrosine phosphatase from Entamoeba histolytica | ||||||
Components | Protein tyrosine phosphatase | ||||||
Keywords | HYDROLASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / parasitic protozoan / dysentery / liver abscess | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2014 Title: Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Authors: Linford, A.S. / Jiang, N.M. / Edwards, T.E. / Sherman, N.E. / Van Voorhis, W.C. / Stewart, L.J. / Myler, P.J. / Staker, B.L. / Petri, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jvi.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jvi.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/3jvi ftp://data.pdbj.org/pub/pdb/validation_reports/jv/3jvi | HTTPS FTP |
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-Related structure data
Related structure data | 3idoSC 3ilyC 3js5C C: citing same article (ref.) S: Starting model for refinement |
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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: 18391.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_153650 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LSE7 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Emerald Biosystems Wizard II screen condition 41, 2.0 M Ammonium sulfate, 0.1 M Tris-HCl pH 7.0, 0.2 M Lithium sulfate, 26.1 mg/mL protein. Crystal tracking ID 203693h5, expression tag ...Details: Emerald Biosystems Wizard II screen condition 41, 2.0 M Ammonium sulfate, 0.1 M Tris-HCl pH 7.0, 0.2 M Lithium sulfate, 26.1 mg/mL protein. Crystal tracking ID 203693h5, expression tag removed with 3C protease, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 13504 / Num. obs: 12964 / % possible obs: 96.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.84 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 5.71 / Num. unique all: 1287 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 30.69 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IDO Resolution: 1.8→42.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.854 / SU B: 5.859 / SU ML: 0.079 / SU R Cruickshank DPI: 0.037 / SU Rfree: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.75 Å2 / Biso mean: 13.914 Å2 / Biso min: 3.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→42.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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