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- PDB-2hl9: SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulf... -

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Basic information

Entry
Database: PDB / ID: 2hl9
TitleSUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfonic acid
ComponentsUbiquitin-like-specific protease 1
KeywordsHYDROLASE
Function / homology
Function and homology information


Ulp1 peptidase / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / G2/M transition of mitotic cell cycle / nuclear envelope / protein-containing complex binding / nucleolus ...Ulp1 peptidase / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / G2/M transition of mitotic cell cycle / nuclear envelope / protein-containing complex binding / nucleolus / proteolysis / nucleus
Similarity search - Function
Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / TATA-Binding Protein / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / TATA-Binding Protein / Papain-like cysteine peptidase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like-specific protease 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXu, Z. / Ng, T.B. / Au, S.W.N.
Citation
Journal: Faseb J. / Year: 2008
Title: Molecular basis of the redox regulation of SUMO proteases: a protective mechanism of intermolecular disulfide linkage against irreversible sulfhydryl oxidation
Authors: Xu, Z. / Lam, L.S.M. / Lam, L.H. / Chau, S.F. / Ng, T.B. / Au, S.W.N.
#1: Journal: Mol.Cell / Year: 2000
Title: Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast
Authors: Mossessova, E. / Lima, C.D.
History
DepositionJul 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like-specific protease 1


Theoretical massNumber of molelcules
Total (without water)25,6981
Polymers25,6981
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.735, 39.448, 55.764
Angle α, β, γ (deg.)90.000, 112.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-83-

HOH

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Components

#1: Protein Ubiquitin-like-specific protease 1 / Ulp1 protease


Mass: 25698.299 Da / Num. of mol.: 1 / Fragment: c-terminal catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q02724, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30%(v/v) pentaerythritol ethoxylate(15/4 EO/OH), 0.05M ammonium sulfate, 100mM hydrogen peroxide , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 27, 2006 / Details: mirror
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→51.62 Å / Num. obs: 19528 / % possible obs: 97.7 % / Redundancy: 7.07 % / Rmerge(I) obs: 0.052 / Χ2: 1.01 / Net I/σ(I): 18.8 / Scaling rejects: 1044
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.87 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.9 / Num. measured all: 10404 / Num. unique all: 1770 / Χ2: 1.1 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUV

1euv


Resolution: 1.9→18.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.44 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.158
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 845 5 %RANDOM
Rwork0.192 ---
all0.194 ---
obs-16793 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.223 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-0.46 Å2
2--1.87 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 113 1884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.024
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_refined_deg1.914
X-RAY DIFFRACTIONr_angle_other_deg1.309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 66 -
Rwork0.287 1151 -
obs-1217 97.52 %

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