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- PDB-6dg4: Structure of the Chaetomium thermophilum Ulp1-like SUMO protease ... -

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Basic information

Entry
Database: PDB / ID: 6dg4
TitleStructure of the Chaetomium thermophilum Ulp1-like SUMO protease catalytic domain
ComponentsUlp1-like SUMO protease
KeywordsHYDROLASE / SUMO hydrolase / ubiquitin-like protease / SMT3 hydrolase / desumoylating enzyme / cysteine protease / SUMO processing enzyme / SMT3 processing enzyme
Function / homologyubiquitin-like protein peptidase activity / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / Specific protease-like protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.442 Å
AuthorsLima, C.D. / Baytshtok, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Discovery and engineering of enhanced SUMO protease enzymes.
Authors: Lau, Y.K. / Baytshtok, V. / Howard, T.A. / Fiala, B.M. / Johnson, J.M. / Carter, L.P. / Baker, D. / Lima, C.D. / Bahl, C.D.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Ulp1-like SUMO protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0106
Polymers29,5421
Non-polymers4685
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-19 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.986, 63.595, 83.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ulp1-like SUMO protease


Mass: 29541.701 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 935-1186)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0004370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RZV7, Ulp1 peptidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.0, 2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2017
RadiationMonochromator: cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 44305 / % possible obs: 97.9 % / Redundancy: 7 % / Biso Wilson estimate: 12.45 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 0.762 / Net I/σ(I): 9.4 / Num. measured all: 310342
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.44-1.466.20.21518780.9730.0910.2340.36285.2
1.46-1.497.20.19922270.9770.0780.2140.36898.5
1.49-1.527.50.18322150.9840.0710.1970.36599.7
1.52-1.557.60.1622220.9870.0610.1720.39599.4
1.55-1.587.70.14622170.9890.0560.1560.403100
1.58-1.627.70.13122270.9930.0510.1410.40299.7
1.62-1.667.50.11722190.9920.0460.1260.4399.6
1.66-1.717.30.10622560.9920.0420.1150.45599.5
1.71-1.766.70.09422100.9930.040.1030.47599.6
1.76-1.816.50.08422280.9940.0360.0920.51299.2
1.81-1.887.50.07322440.9960.0290.0790.57199.4
1.88-1.957.50.06522100.9960.0260.070.63198.7
1.95-2.047.10.05922030.9970.0240.0640.73297.9
2.04-2.156.80.05222230.9980.0220.0560.8598.2
2.15-2.296.50.04922280.9970.0210.0540.94197.9
2.29-2.4660.04621910.9980.0210.0511.08796.8
2.46-2.716.20.04322350.9980.0190.0471.13897
2.71-3.170.04322300.9980.0180.0471.44596.8
3.1-3.916.80.0422410.9980.0170.0441.85796.8
3.91-506.60.03924010.9980.0170.0432.05397.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EUV

1euv


Resolution: 1.442→41.842 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 13.15
RfactorNum. reflection% reflection
Rfree0.1481 1999 4.52 %
Rwork0.1181 --
obs0.1195 44240 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.35 Å2 / Biso mean: 19.2422 Å2 / Biso min: 6.65 Å2
Refinement stepCycle: final / Resolution: 1.442→41.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 50 461 2492
Biso mean--56.58 34.93 -
Num. residues----253
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4423-1.47830.19531390.14082939307897
1.4783-1.51830.18741420.1212996313899
1.5183-1.5630.17161410.10729833124100
1.563-1.61350.17051440.105630303174100
1.6135-1.67110.15131430.10123028317199
1.6711-1.7380.12961430.104330203163100
1.738-1.81710.14761430.1053014315799
1.8171-1.91290.14441450.10883054319999
1.9129-2.03280.14551400.10842958309898
2.0328-2.18970.13771430.10563038318198
2.1897-2.41010.11891410.10872976311797
2.4101-2.75880.1491410.11422995313697
2.7588-3.47550.1511450.12673037318297
3.4755-41.85960.15151490.13833173332297

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