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- PDB-2ayv: Crystal structure of a putative ubiquitin-conjugating enzyme E2 f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ayv | ||||||
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Title | Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii | ||||||
![]() | ubiquitin-conjugating enzyme E2 | ||||||
![]() | LIGASE / Structural Genomics / Structural Genomics Consortium / ubiquitin / ubiquitin-conjugating enzyme / SGC | ||||||
Function / homology | Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Roll / Alpha Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Arrowsmith, C. ...Tempel, W. / Dong, A. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Wasney, G. / Kozieradzki, I. / Vedadi, M. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Bochkarev, A. / Hui, R. / Amani, M. / 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 42 | MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 7.37 (7.62 B<40) BAD ROTAMERS : 3.4% 4/119 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/146 (TARGET 0.2%) RAMACHANDRAN FAVORED : 97.3% 142/146 (TARGET 98.0%) |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.7 KB | Display | ![]() |
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PDB format | ![]() | 29.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.2 KB | Display | ![]() |
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Full document | ![]() | 402.1 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1txjC ![]() 1xccC ![]() 1y6zC ![]() 1z6gC ![]() 1z7dC ![]() 1z81C ![]() 1zo2C ![]() 2a22C ![]() 2a4aC ![]() 2aifC ![]() 2amxC ![]() 2aqwC ![]() 2av4C ![]() 2awpC ![]() 2b71C ![]() 2bddC ![]() 2f4zC ![]() 2fdsC ![]() 2ffcC ![]() 2fo3C ![]() 2fu0C ![]() 2ghiC ![]() 2h1rC ![]() 2h2yC ![]() 2h66C ![]() 2hjrC ![]() 2hteC ![]() 2hvgC ![]() 3pggC ![]() 3tb2C ![]() 1x23S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18815.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-UNX / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 6, 2005 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→20 Å / Num. obs: 12360 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.038 / Χ2: 1.021 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | Rfactor: 0.45 / Cor.coef. Fo:Fc: 0.578
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X23 Resolution: 2.001→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.275 / WRfactor Rwork: 0.26 / SU B: 12.897 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.822 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.7452 Å / Origin y: 69.7416 Å / Origin z: 76.6636 Å
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Refinement TLS group | Selection: ALL |