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- PDB-4ii3: Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ii3 | ||||||
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Title | Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg | ||||||
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![]() | LIGASE / Rossmann-like Fold / ubiquitin-like fold / Ubiquitin activating enzyme activity / ATP binding / Ligase activity / ATP/Mg binding / Ubiquitin E2 binding | ||||||
Function / homology | ![]() Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ubiquitin-dependent protein catabolic process / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA damage response / nucleolus / magnesium ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Olsen, S.K. / Lima, C.D. | ||||||
![]() | ![]() Title: Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. Authors: Olsen, S.K. / Lima, C.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 434.7 KB | Display | ![]() |
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PDB format | ![]() | 342.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 78.9 KB | Display | |
Data in CIF | ![]() | 105.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ii2C ![]() 3cmmS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 111764.047 Da / Num. of mol.: 2 / Fragment: Uba1, UNP residues 13-1012 Source method: isolated from a genetically manipulated source Details: N-terminal SMT3 fusion (Ulp-cleavable) Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 Gene: ptr3, SPBC1604.21c, SPBC211.09, Ubiquitin activating enzyme 1 (Uba1) Plasmid: pSMT3 / Production host: ![]() ![]() #2: Protein | Mass: 10740.132 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: strain 972 / ATCC 24843 / Gene: ubi2 / Plasmid: pET-28 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 165 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Cacodylate, 0.2M Calcium Acetate, 11.5% Peg8000, 3% 1,5 diaminopentane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 108 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.4 % / Av σ(I) over netI: 8 / Number: 189068 / Rmerge(I) obs: 0.113 / Χ2: 1.07 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 55035 / % possible obs: 95.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.9→50 Å / Num. all: 57810 / Num. obs: 55035 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Χ2: 1.07 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CMM Resolution: 2.9→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 11.0687 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.35 Å2 / Biso mean: 61.8011 Å2 / Biso min: 2.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 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: 10
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Xplor file |
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