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Yorodumi- PDB-2f4z: Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f4z | ||||||
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Title | Toxoplasma gondii ubiquitin conjugating enzyme TgTwinScan_2721- E2 domain | ||||||
Components | TgTwinScan_2721 - E2 domain | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin conjugating TgTwinScan_2721 / Structural Genomics Consortium / SGC | ||||||
Function / homology | Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | 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) | ||||||
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. / 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 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f4z.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f4z.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 2f4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4z ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4z | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Toxoplasma gondii (eukaryote) / Plasmid: P28-LIC-THROMBIN DERIVED FROM SOURCE 9 PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-UNX / | #4: 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: 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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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