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Open data
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Basic information
Entry | Database: PDB / ID: 3a4s | ||||||
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Title | The crystal structure of the SLD2:Ubc9 complex | ||||||
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![]() | LIGASE/TRNASCRIPTION / ubiquitin fold / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sekiyama, N. / Arita, K. / Ikeda, Y. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M. | ||||||
![]() | ![]() Title: Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45 Authors: Sekiyama, N. / Arita, K. / Ikeda, Y. / Hashiguchi, K. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.8 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a4rSC ![]() 1a3sS 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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Unit cell |
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Components
#1: Protein | Mass: 18442.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P63279, ![]() #2: Protein | Mass: 8677.913 Da / Num. of mol.: 2 / Fragment: SLD2, Ubiquitin-like domain, residues 339-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Sequence details | THIS COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.23 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, ...Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.58→46.4 Å / Num. obs: 13920 / % possible obs: 93.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.93 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.2 / Num. measured all: 645440 |
Reflection shell | Resolution: 2.58→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.196 / % possible all: 73.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entries; 1A3S and 3A4R Resolution: 2.7→46.366 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.776 / SU ML: 0.41 / σ(F): 1.98 / Phase error: 29.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.944 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.02 Å2 / Biso mean: 42.69 Å2 / Biso min: 11.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46.366 Å
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Refine LS restraints |
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LS refinement shell |
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