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- PDB-5lnb: Crystal structure of the de-sumoylating protease -

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Basic information

Entry
Database: PDB / ID: 5lnb
TitleCrystal structure of the de-sumoylating protease
ComponentsUbiquitin-like-specific protease 2
KeywordsHYDROLASE / Protease / de-sumoylation
Function / homology
Function and homology information


SUMO is proteolytically processed / plasmid maintenance / deSUMOylase activity / protein desumoylation / transcription elongation factor activity / chromosome condensation / Major pathway of rRNA processing in the nucleolus and cytosol / mitotic spindle assembly checkpoint signaling / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...SUMO is proteolytically processed / plasmid maintenance / deSUMOylase activity / protein desumoylation / transcription elongation factor activity / chromosome condensation / Major pathway of rRNA processing in the nucleolus and cytosol / mitotic spindle assembly checkpoint signaling / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / chromatin / proteolysis / nucleus
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-like-specific protease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsEckhoff, J. / Dohmen, J. / Pichlo, C. / Baumann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: To Be Published
Title: Crystal structure of the de-sumoylating protease
Authors: Eckhoff, J. / Dohmen, J. / Pichlo, C. / Baumann, U.
History
DepositionAug 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ubiquitin-like-specific protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6732
Polymers36,6141
Non-polymers591
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-0 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 55.580, 172.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-like-specific protease 2


Mass: 36613.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protease domain residues 427 to 704
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ULP2, SMT4, YIL031W / Details (production host): pMALc2X / Production host: Escherichia coli (E. coli) / References: UniProt: P40537, Ulp1 peptidase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate, 20 % PEG 3350, protein concentration 3 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0644 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 23, 2015 / Details: mirror
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0644 Å / Relative weight: 1
ReflectionResolution: 2.26→100 Å / Num. obs: 36221 / % possible obs: 97.4 % / Redundancy: 44.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 33.82
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 3.44 / % possible all: 77.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→86.39 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.89
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 3137 9.04 %random
Rwork0.1571 ---
obs0.1607 34694 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→86.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 4 199 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062230
X-RAY DIFFRACTIONf_angle_d0.6963007
X-RAY DIFFRACTIONf_dihedral_angle_d10.8511349
X-RAY DIFFRACTIONf_chiral_restr0.048331
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.28181230.2131246X-RAY DIFFRACTION84
2.3359-2.37420.21551290.19431298X-RAY DIFFRACTION91
2.3742-2.41520.22641430.18251426X-RAY DIFFRACTION96
2.4152-2.45910.20281340.17831393X-RAY DIFFRACTION100
2.4591-2.50640.22761430.16631504X-RAY DIFFRACTION100
2.5064-2.55760.19921440.17461430X-RAY DIFFRACTION100
2.5576-2.61320.23931460.17471466X-RAY DIFFRACTION100
2.6132-2.6740.2021410.1531484X-RAY DIFFRACTION100
2.674-2.74090.20121400.15771422X-RAY DIFFRACTION100
2.7409-2.8150.22691470.15921470X-RAY DIFFRACTION100
2.815-2.89780.17621470.1611443X-RAY DIFFRACTION100
2.8978-2.99130.19711450.15911445X-RAY DIFFRACTION100
2.9913-3.09830.25291460.17081456X-RAY DIFFRACTION100
3.0983-3.22230.18741460.17191451X-RAY DIFFRACTION100
3.2223-3.3690.2151490.15731443X-RAY DIFFRACTION100
3.369-3.54660.19321440.1561465X-RAY DIFFRACTION100
3.5466-3.76880.23531410.14881450X-RAY DIFFRACTION100
3.7688-4.05980.13581460.13461450X-RAY DIFFRACTION100
4.0598-4.46830.1581460.12381449X-RAY DIFFRACTION100
4.4683-5.11480.15051450.12371467X-RAY DIFFRACTION100
5.1148-6.44380.20631460.16551442X-RAY DIFFRACTION100
6.4438-86.4510.19771460.17521457X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5623-0.68131.03872.6354-1.56135.2232-0.0848-0.5183-0.00390.34990.14740.1263-0.1967-0.16-0.03440.2373-0.02920.00760.2842-0.0310.18285.710119.280270.2965
24.09151.22350.70331.35930.0781.3597-0.030.4395-0.1695-0.03750.03290.04740.01340.07240.0090.19510.00190.01010.2192-0.04010.15472.289913.144352.5075
32.54870.8506-1.7081.0272-1.91114.47280.1097-0.3690.06840.2207-0.2453-0.0539-0.47680.56110.14220.282-0.018-0.02480.1762-0.04470.265712.139125.186966.4808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 22 through 83 )
2X-RAY DIFFRACTION2chain 'B' and (resid 84 through 232 )
3X-RAY DIFFRACTION3chain 'B' and (resid 233 through 299 )

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