SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / RHOF GTPase cycle / SUMOylation of RNA binding proteins ...SUMO-specific endopeptidase activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / deSUMOylase activity / protein desumoylation / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / RHOF GTPase cycle / SUMOylation of RNA binding proteins / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / regulation of mRNA stability / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / apoptotic signaling pathway / SUMOylation of intracellular receptors / PML body / Formation of Incision Complex in GG-NER / protein tag activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / nuclear membrane / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / ubiquitin protein ligase binding / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function
Mass: 9325.474 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT, RESIDUES 15-95 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61956
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
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 6.04 Å3/Da / Density % sol: 79.46 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 3.2→120 Å / Num. obs: 13469 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19
Reflection shell
Resolution: 3.2→3.3 Å / Redundancy: 8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
SCALA
datascaling
CCP4
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.98 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.913 / SU B: 54.553 / SU ML: 0.378 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY AN OVERALL B FACTOR REFINED THIS REPLACES PREVIOUS ENTRY WHICH HAD SEQUENCE CONFLICTS. THERE IS COVALENT LINK BETWEEN CYS A 603 (SENP1) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY AN OVERALL B FACTOR REFINED THIS REPLACES PREVIOUS ENTRY WHICH HAD SEQUENCE CONFLICTS. THERE IS COVALENT LINK BETWEEN CYS A 603 (SENP1) AND GLY B 92 (SUMO) THE DICTIONARY IS INCLUDED IN ENTRY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.288
714
5 %
RANDOM
Rwork
0.272
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obs
0.273
13468
99 %
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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