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- PDB-2f4z: Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f4z | ||||||
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Title | Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain | ||||||
![]() | TgTwinScan_2721 - E2 domain | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin conjugating TgTwinScan_2721 / Structural Genomics Consortium / SGC | ||||||
Function / homology | Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, A. / Lew, J. / Zhao, Y. / Melone, M. / Alam, Z. / Kozieradski, I. / Wasney, G. / Vedadi, M. / Sundstrom, M. / Weigelt, J. ...Dong, A. / Lew, J. / Zhao, Y. / Melone, M. / Alam, Z. / Kozieradski, I. / Wasney, G. / Vedadi, M. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J. / 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. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / 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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Remark 300 | Author states that biological unit for the protein is not yet known | ||||||
Remark 999 | Sequence No suitable database references were found at time of processing |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ![]() 2fdsC ![]() 2ffcC ![]() 2fo3C ![]() 2fu0C ![]() 2ghiC ![]() 2h1rC ![]() 2h2yC ![]() 2h66C ![]() 2hjrC ![]() 2hteC ![]() 2hvgC ![]() 3pggC ![]() 3tb2C ![]() 2bepS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21504.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-UNX / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 8.4 Details: 32% Peg 1500, 0.2 M MgCl2, 0.1 M Tris pH 8.4, 10 mM Spermidine, VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2005 / Details: VeriMax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. all: 23386 / Num. obs: 23386 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.12→2.16 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.22 / Num. unique all: 1143 / Rsym value: 0.729 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BEP Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.71 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.114→2.169 Å / Total num. of bins used: 20
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