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- PDB-5ubw: Structure of catalytic domain of Ssel -

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Basic information

Entry
Database: PDB / ID: 5ubw
TitleStructure of catalytic domain of Ssel
ComponentsDeubiquitinase SseL
KeywordsHYDROLASE / UCH family / Salmonella / deubiquitinases
Function / homology
Function and homology information


cysteine-type peptidase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region
Similarity search - Function
: / : / ElaD/SseL-like C-terminal / ElaD/SseL N-terminal domain
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsShrestha, R. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of catalytic domain of Ssel
Authors: Shrestha, R. / Das, C.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deubiquitinase SseL
B: Deubiquitinase SseL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1293
Polymers42,0672
Non-polymers621
Water39622
1
A: Deubiquitinase SseL


Theoretical massNumber of molelcules
Total (without water)21,0341
Polymers21,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Deubiquitinase SseL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0962
Polymers21,0341
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.819, 64.983, 56.884
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Deubiquitinase SseL / Deubiquitinating enzyme / DUB / Deubiquitinating protease / Salmonella secreted effector L


Mass: 21033.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sseL, STM2287 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZNG2, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5 and 1.5 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.394→54.6 Å / Num. obs: 14585 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.394→2.44 Å / Redundancy: 3.8 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAF

5haf


Resolution: 2.394→42.604 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.88
RfactorNum. reflection% reflection
Rfree0.3044 725 5.03 %
Rwork0.25 --
obs0.2526 14424 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.394→42.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 4 22 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032734
X-RAY DIFFRACTIONf_angle_d0.5673712
X-RAY DIFFRACTIONf_dihedral_angle_d14.003961
X-RAY DIFFRACTIONf_chiral_restr0.023444
X-RAY DIFFRACTIONf_plane_restr0.004472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.394-2.57880.34581340.32632603X-RAY DIFFRACTION95
2.5788-2.83830.38441540.32762740X-RAY DIFFRACTION100
2.8383-3.24890.41421320.31062779X-RAY DIFFRACTION100
3.2489-4.09270.31211510.23642779X-RAY DIFFRACTION100
4.0927-42.61050.24111540.20872798X-RAY DIFFRACTION99

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