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- PDB-3g06: The Salmonella Virulence Effector SspH2 Functions As A Novel E3 Ligase -

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Basic information

Entry
Database: PDB / ID: 3g06
TitleThe Salmonella Virulence Effector SspH2 Functions As A Novel E3 Ligase
ComponentsSspH2 (Leucine-rich repeat protein)
KeywordsLIGASE / E3 Ubiquitin Ligase / Leucine Rich Repeat Domain / Type Three effector / Salmonella virulence factor / SPI-2
Function / homology
Function and homology information


positive regulation of plant-type hypersensitive response / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / protein secretion by the type III secretion system / : / catalytic activity / positive regulation of interleukin-8 production / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell cytoplasm ...positive regulation of plant-type hypersensitive response / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / protein secretion by the type III secretion system / : / catalytic activity / positive regulation of interleukin-8 production / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell cytoplasm / protein ubiquitination / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SspH2 / E3 ubiquitin-protein ligase SspH2
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQuezada, C.M. / Stebbins, C.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases.
Authors: Quezada, C.M. / Hicks, S.W. / Galan, J.E. / Stebbins, C.E.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
A: SspH2 (Leucine-rich repeat protein)


Theoretical massNumber of molelcules
Total (without water)68,5371
Polymers68,5371
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.885, 76.885, 281.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SspH2 (Leucine-rich repeat protein)


Mass: 68536.992 Da / Num. of mol.: 1 / Fragment: LRR + NEL Domain, Residues 166-783
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: Salmonella LT2 / Gene: sspH2, STM2241 / Plasmid: pCDF-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9RPH0, UniProt: P0CE12*PLUS, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 8-10% PEG5K, 5% tacsimate, 0.1M HEPES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 63141 / Num. obs: 63141 / % possible obs: 98.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 35 Å2 / Net I/σ(I): 23
Reflection shellHighest resolution: 1.9 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.85 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN TEH RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 3369 5.1 %RANDOM
Rwork0.2186 ---
obs0.22094 63141 98.14 %-
all-63141 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.976 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 0 406 5069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224753
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9886468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2775598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89824.378201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06715822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0211534
X-RAY DIFFRACTIONr_chiral_restr0.1260.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213548
X-RAY DIFFRACTIONr_mcbond_it1.041.53008
X-RAY DIFFRACTIONr_mcangle_it1.87624849
X-RAY DIFFRACTIONr_scbond_it3.4231745
X-RAY DIFFRACTIONr_scangle_it5.5954.51619
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 228 -
Rwork0.448 4468 -
obs-4468 95.84 %

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