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

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Basic information

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


Ulp1 peptidase / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / 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: 2.1 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 5, 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

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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)25,6661
Polymers25,6661
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)105.089, 40.328, 55.379
Angle α, β, γ (deg.)90.000, 112.020, 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: 25666.301 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

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% w/v PEG 3350, 0.2M NaCl and post-soaked in 50mM DTT for 48 hours, 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 27, 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→51.367 Å / Num. obs: 14736 / % possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.5 / Num. measured all: 6418 / Num. unique all: 2117 / Rsym value: 0.493 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUV

1euv


Resolution: 2.1→51.367 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.881 / SU B: 5.161 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.22
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 660 5.2 %RANDOM
Rwork0.216 ---
all0.218 ---
obs-12780 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.401 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.69 Å2
2--1.53 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 116 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221818
X-RAY DIFFRACTIONr_bond_other_d0.0020.021643
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9612454
X-RAY DIFFRACTIONr_angle_other_deg1.18933830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68824.2789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3821512
X-RAY DIFFRACTIONr_chiral_restr0.1460.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_nbd_refined0.2090.2388
X-RAY DIFFRACTIONr_nbd_other0.1940.21633
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2872
X-RAY DIFFRACTIONr_nbtor_other0.0890.21123
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.380.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.24
X-RAY DIFFRACTIONr_mcbond_it1.7981.51389
X-RAY DIFFRACTIONr_mcbond_other0.3791.5442
X-RAY DIFFRACTIONr_mcangle_it2.16421769
X-RAY DIFFRACTIONr_scbond_it3.2763834
X-RAY DIFFRACTIONr_scangle_it4.3674.5685
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 47 -
Rwork0.275 877 -
obs-924 100 %

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