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- PDB-9h6w: Crystal structure of the Salmonella effector SspH1 -

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Basic information

Entry
Database: PDB / ID: 9h6w
TitleCrystal structure of the Salmonella effector SspH1
ComponentsE3 ubiquitin-protein ligase SspH1
KeywordsLIGASE / E3 ubiquitin ligase / Salmonella effector protein / NEL proteins
Function / homology
Function and homology information


protein secretion by the type III secretion system / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / protein ubiquitination / host cell nucleus / extracellular region
Similarity search - Function
Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / : / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / E3 ubiquitin-protein ligase SspH1
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKennedy, C.R. / Esposito, D. / House, D. / Rittinger, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2075 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T014547/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the Salmonella effector SspH1
Authors: Kennedy, C.R. / Esposito, D. / House, D. / Rittinger, K.
History
DepositionOct 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SspH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7542
Polymers59,6041
Non-polymers1501
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, SAXS shows the protein is monomeric in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area25470 Å2
2
A: E3 ubiquitin-protein ligase SspH1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)358,52412
Polymers357,6246
Non-polymers9016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
crystal symmetry operation12_545x,x-y-1,-z1
Buried area26080 Å2
ΔGint-59 kcal/mol
Surface area127760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.772, 170.772, 94.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase SspH1 / RING-type E3 ubiquitin transferase SspH1 / Salmonella secreted protein H1 / Secreted effector protein SspH1


Mass: 59603.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 160 amino acids have been deleted from the construct.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sspH1, STM14_1483 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D0ZVG2, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.225 M sodium tartrate, 22% PEG 3350, 11 mM sarcosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 0.62 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.9→58.31 Å / Num. obs: 18583 / % possible obs: 99.8 % / Redundancy: 39.6 % / Biso Wilson estimate: 74.61 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.4992 / Rpim(I) all: 0.07988 / Rrim(I) all: 0.5056 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 73343 / CC1/2: 0.416 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
REFMACRefmac_5.8refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→58.31 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3158 900 4.85 %
Rwork0.2595 --
obs0.262 18545 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→58.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 10 44 4247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014282
X-RAY DIFFRACTIONf_angle_d0.3525826
X-RAY DIFFRACTIONf_dihedral_angle_d10.7991583
X-RAY DIFFRACTIONf_chiral_restr0.032667
X-RAY DIFFRACTIONf_plane_restr0.002766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.080.44021640.37032845X-RAY DIFFRACTION100
3.08-3.320.41991440.35452877X-RAY DIFFRACTION100
3.32-3.650.36231380.2892912X-RAY DIFFRACTION100
3.65-4.180.32481250.25862944X-RAY DIFFRACTION100
4.18-5.270.29961530.23722961X-RAY DIFFRACTION100
5.27-58.310.26881760.22193106X-RAY DIFFRACTION100

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