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- PDB-6iai: StoD is a novel Salmonella Typhi type III secretion system E3 ubi... -

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Basic information

Entry
Database: PDB / ID: 6iai
TitleStoD is a novel Salmonella Typhi type III secretion system E3 ubiquitin ligase effector
ComponentsProtein of uncharacterized function (DUF1076)
KeywordsPROTEIN BINDING / salmonella T3SS effector ubiquitin ligase
Function / homologyEffector protein NleG / Effector protein NleG superfamily / Effector protein NleG / biological process involved in symbiotic interaction / ubiquitin-protein transferase activity / DUF1076 domain-containing protein
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.54 Å
AuthorsMcDowell, M.A. / Lea, S.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust100298/Z/12/Z United Kingdom
Wellcome Trust107057/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K001515/1 United Kingdom
CitationJournal: Life Sci Alliance / Year: 2019
Title: The S . Typhi effector StoD is an E3/E4 ubiquitin ligase which binds K48- and K63-linked diubiquitin.
Authors: McDowell, M.A. / Byrne, A.M. / Mylona, E. / Johnson, R. / Sagfors, A. / Crepin, V.F. / Lea, S. / Frankel, G.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 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: Protein of uncharacterized function (DUF1076)
B: Protein of uncharacterized function (DUF1076)
C: Protein of uncharacterized function (DUF1076)
D: Protein of uncharacterized function (DUF1076)


Theoretical massNumber of molelcules
Total (without water)55,5864
Polymers55,5864
Non-polymers00
Water63135
1
A: Protein of uncharacterized function (DUF1076)


Theoretical massNumber of molelcules
Total (without water)13,8971
Polymers13,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein of uncharacterized function (DUF1076)


Theoretical massNumber of molelcules
Total (without water)13,8971
Polymers13,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein of uncharacterized function (DUF1076)


Theoretical massNumber of molelcules
Total (without water)13,8971
Polymers13,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein of uncharacterized function (DUF1076)


Theoretical massNumber of molelcules
Total (without water)13,8971
Polymers13,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.960, 92.960, 156.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein
Protein of uncharacterized function (DUF1076) / StoD


Mass: 13896.517 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY1076, STY1076, t1865, NCTC8385_01041 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Z7T2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 59.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 60% 0.9 M Na malonate, 0.5% Jeffamine, 0.1M HEPES pH 6.5

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 23, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.54→34.65 Å / Num. obs: 23299 / % possible obs: 99.8 % / Redundancy: 26.1 % / Biso Wilson estimate: 61.89 Å2 / Net I/σ(I): 30.8
Reflection shellResolution: 2.54→2.61 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
xia2data reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.54→34.65 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9114 / SU R Cruickshank DPI: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.343 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1196 5.14 %RANDOM
Rwork0.2158 ---
obs0.2173 23254 99.86 %-
Displacement parametersBiso mean: 54.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.4995 Å20 Å20 Å2
2--6.4995 Å20 Å2
3----12.9989 Å2
Refine analyzeLuzzati coordinate error obs: 0.365 Å
Refinement stepCycle: 1 / Resolution: 2.54→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 35 3530
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154779HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1317SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes520HARMONIC5
X-RAY DIFFRACTIONt_it3550HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion459SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3876SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.65 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2997 149 5.35 %
Rwork0.2523 2637 -
all0.2548 2786 -
obs--99.86 %

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