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Open data
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Basic information
Entry | Database: PDB / ID: 2iyc | ||||||
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Title | SENP1 native structure | ||||||
![]() | SENTRIN-SPECIFIC PROTEASE 1 | ||||||
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Function / homology | ![]() SUMO-specific endopeptidase activity / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / RHOF GTPase cycle / protein sumoylation / regulation of mRNA stability / apoptotic signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, C. / Naismith, J.H. | ||||||
![]() | #1: ![]() Title: The Structure of Senp1 Sumo-2 Co-Complex Suggests a Structural Basis for Discrimination between Sumo Paralogues During Processing Authors: Shen, L. / Dong, C. / Liu, H. / Naismith, J.H. / Hay, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 81.1 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 430 - 640 / Label seq-ID: 12 - 222
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Components
#1: Protein | Mass: 26932.211 Da / Num. of mol.: 2 / Fragment: CATALYTIC FRAGMENT, RESIDUES 419-643 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9P0U3, ![]() #2: Water | ChemComp-HOH / | ![]() Sequence details | THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED ...THE EXTRA RESIDUE AT POSITION 593 IN CHAINS A AND B IS A KNOWN CONFLICT IN UNIPROT AND IS DESCRIBED IN PUBMED ID: 12477932. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.22 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.45→54 Å / Num. obs: 21832 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THIS REPLACES PREVIOUS ENTRY WHICH WHICH HAD SEQUENCE CONFLICTS. THE BOND DEVIATIONS FOR GLU AND HIS ARE CAUSED BY DENSITY ON THE SYMMETRY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THIS REPLACES PREVIOUS ENTRY WHICH WHICH HAD SEQUENCE CONFLICTS. THE BOND DEVIATIONS FOR GLU AND HIS ARE CAUSED BY DENSITY ON THE SYMMETRY POSITION. THIS SUCKS THE SIDE CHAINS IN. A WATER HERE IS REJECTED BY ARWARP ETC.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→53 Å
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Refine LS restraints |
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