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- PDB-2hl8: SUMO protease Ulp1 with the catalytic cysteine oxidized to a sulf... -

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Basic information

Entry
Database: PDB / ID: 2hl8
TitleSUMO protease Ulp1 with the catalytic cysteine oxidized to a sulfinic 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 / nucleolus / proteolysis / nucleus
Similarity search - Function
Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / 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 / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / 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: 2 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 1.2Nov 12, 2014Group: Other
Revision 1.3Oct 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,6821
Polymers25,6821
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.936, 40.189, 55.371
Angle α, β, γ (deg.)90.000, 112.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 25682.299 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-2 / 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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20%(w/v) PEG 3350, 0.2M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2006 / Details: mirrors
RadiationMonochromator: VariMax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→44.63 Å / Num. obs: 14290 / % possible obs: 97.2 % / Redundancy: 7.35 % / Rmerge(I) obs: 0.073 / Χ2: 0.99 / Net I/σ(I): 16.3 / Scaling rejects: 794
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.28 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 5.1 / Num. measured all: 10146 / Num. unique all: 1393 / Χ2: 1.01 / % possible all: 95.5

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata 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: 2→19.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.897 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.179
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 711 5 %RANDOM
Rwork0.192 ---
all0.194 ---
obs-14277 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.135 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0.02 Å2
2--1.06 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 0 116 1888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.024
X-RAY DIFFRACTIONr_bond_other_d0.004
X-RAY DIFFRACTIONr_angle_refined_deg1.912
X-RAY DIFFRACTIONr_angle_other_deg1.054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.599
X-RAY DIFFRACTIONr_chiral_restr0.129
X-RAY DIFFRACTIONr_gen_planes_refined
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 52 -
Rwork0.245 976 -
obs-1028 95.36 %

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