+Open data
-Basic information
Entry | Database: PDB / ID: 3tb2 | ||||||
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Title | 1-Cys peroxidoxin from Plasmodium Yoelli | ||||||
Components | 1-Cys peroxiredoxin | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium yoelii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Qiu, W. / Artz, J.D. / Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. ...Qiu, W. / Artz, J.D. / Vedadi, M. / Sharma, S. / Houston, S. / Lew, J. / Wasney, G. / Amani, M. / Xu, X. / Bray, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Hui, R. / Bochkarev, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2007 Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J.D. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, ...Authors: Vedadi, M. / Lew, J. / Artz, J.D. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tb2.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tb2.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/3tb2 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/3tb2 | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25360.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Pet15 Tev Is a Modification of Pet15b (novagen) with Thrombin Site Replaced with Tev Site. Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Gene: py04285 / Plasmid: pET15-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86SB3 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: # 22% Peg 3350, 0.1M Bis-Tris pH 5.5, 0.2M Lithium Sulfate, 5% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2004 |
Radiation | Monochromator: UNKNOWN / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 56255 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 44.44 Å2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.3→78.42 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9373 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 43.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.223 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→78.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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