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- PDB-4jue: Crystal structure of Plasmodium falciparum ubiquitin conjugating ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jue | ||||||
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Title | Crystal structure of Plasmodium falciparum ubiquitin conjugating enzyme UBC9 | ||||||
![]() | Ubiquitin conjugating enzyme UBC9 | ||||||
![]() | PROTEIN BINDING / SUMO / E2 enzyme | ||||||
Function / homology | ![]() SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMO conjugating enzyme activity / ligase activity / protein sumoylation / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reiter, K.H. / Boucher, L.E. / Bosch, J. / Matunis, J.M. | ||||||
![]() | ![]() Title: Identification of Biochemically Distinct Properties of the Small Ubiquitin-related Modifier (SUMO) Conjugation Pathway in Plasmodium falciparum. Authors: Reiter, K. / Mukhopadhyay, D. / Zhang, H. / Boucher, L.E. / Kumar, N. / Bosch, J. / Matunis, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.5 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 18360.049 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: PF3D7_0915100, PFI0740c / Plasmid: WTPfUbc9-pGex4T1 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M NaF, 20% PEG3350 Cryo: 30% PEG3350, 10% glycerol, 0.2M NaF, 100mM glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2010 |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.49 |
Reflection | Resolution: 1.85→25 Å / Num. all: 53373 / Num. obs: 53373 / % possible obs: 93.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Balbes automatic selection Resolution: 1.851→24.978 Å / σ(F): 1.37 / Phase error: 18.05 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.851→24.978 Å
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Refine LS restraints |
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LS refinement shell |
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