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Yorodumi- PDB-2ayv: Crystal structure of a putative ubiquitin-conjugating enzyme E2 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ayv | ||||||
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Title | Crystal structure of a putative ubiquitin-conjugating enzyme E2 from Toxoplasma gondii | ||||||
Components | ubiquitin-conjugating enzyme E2 | ||||||
Keywords | LIGASE / Structural Genomics / Structural Genomics Consortium / ubiquitin / ubiquitin-conjugating enzyme / 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 / molecular replacement / Resolution: 2.001 Å | ||||||
Authors | 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) | ||||||
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 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%) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ayv.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ayv.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ayv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ayv_validation.pdf.gz | 402.2 KB | Display | wwPDB validaton report |
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Full document | 2ayv_full_validation.pdf.gz | 402.1 KB | Display | |
Data in XML | 2ayv_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 2ayv_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/2ayv ftp://data.pdbj.org/pub/pdb/validation_reports/ay/2ayv | 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 (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
#1: Protein | Mass: 18815.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: p15TvL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: ubiquitin-protein ligase | ||
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#2: Chemical | ChemComp-UNX / #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: 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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||
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: molecular replacement | ||||||
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Phasing MR | Rfactor: 0.45 / Cor.coef. Fo:Fc: 0.578
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |