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- PDB-5haf: Structure of Salmonella enterica effector protein SseL -

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Basic information

Entry
Database: PDB / ID: 5haf
TitleStructure of Salmonella enterica effector protein SseL
ComponentsDeubiquitinase SseL
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase
Function / homologycysteine-type peptidase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / : / Deubiquitinase SseL
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
CitationJournal: Mol.Cell / Year: 2016
Title: The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases.
Authors: Pruneda, J.N. / Durkin, C.H. / Geurink, P.P. / Ovaa, H. / Santhanam, B. / Holden, D.W. / Komander, D.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)75,7585
Polymers75,6412
Non-polymers1173
Water1,72996
1
A: Deubiquitinase SseL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8993
Polymers37,8211
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deubiquitinase SseL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8602
Polymers37,8211
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.009, 113.009, 166.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

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


Mass: 37820.520 Da / Num. of mol.: 2 / Fragment: UNP residues 24-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sseL, STM2287 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZNG2, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, 1.6 M Dipotassium phosphate (pH 8.7)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→84.39 Å / Num. obs: 33454 / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→84.386 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1693 5.07 %
Rwork0.1869 --
obs0.189 33405 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→84.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 3 96 4967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034952
X-RAY DIFFRACTIONf_angle_d0.6696728
X-RAY DIFFRACTIONf_dihedral_angle_d11.9491746
X-RAY DIFFRACTIONf_chiral_restr0.045796
X-RAY DIFFRACTIONf_plane_restr0.002869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.77970.33221210.28652638X-RAY DIFFRACTION100
2.7797-2.86940.32711490.27382626X-RAY DIFFRACTION100
2.8694-2.97190.29781540.25572646X-RAY DIFFRACTION100
2.9719-3.09090.30471260.24952617X-RAY DIFFRACTION99
3.0909-3.23160.36211440.22182600X-RAY DIFFRACTION98
3.2316-3.4020.22881320.19232641X-RAY DIFFRACTION100
3.402-3.61520.20941450.16662644X-RAY DIFFRACTION100
3.6152-3.89430.18461620.15142631X-RAY DIFFRACTION99
3.8943-4.28620.18171500.12652612X-RAY DIFFRACTION98
4.2862-4.90630.1691310.13142689X-RAY DIFFRACTION100
4.9063-6.18120.18991500.17992614X-RAY DIFFRACTION98
6.1812-84.42690.24211290.21592754X-RAY DIFFRACTION99
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)
11.1494-1.33220.13283.1292-0.51690.5098-0.0988-0.2014-0.13730.2320.0629-0.0701-0.00260.06210.01820.31640.0130.02680.34360.04020.216817.21354.8333109.2077
22.0043-1.4620.83431.8016-0.66011.2005-0.06-0.0870.05720.03560.0766-0.1616-0.0029-0.0469-0.02770.24410.0107-0.00290.2683-0.04480.196637.550448.8987.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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