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- PDB-3l3p: Crystal structure of the C-terminal domain of Shigella type III e... -

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Basic information

Entry
Database: PDB / ID: 3l3p
TitleCrystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap
ComponentsIpaH9.8
KeywordsLIGASE / E3 ligase / Domain swap / CXD motif
Function / homology
Function and homology information


symbiont-mediated perturbation of host NF-kappaB cascade / symbiont-mediated suppression of host inflammatory response / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host defenses / protein K27-linked ubiquitination / host cell cytosol / : / protein autoubiquitination / protein K48-linked ubiquitination ...symbiont-mediated perturbation of host NF-kappaB cascade / symbiont-mediated suppression of host inflammatory response / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host defenses / protein K27-linked ubiquitination / host cell cytosol / : / protein autoubiquitination / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell nucleus / extracellular region / identical protein binding
Similarity search - Function
Shigella T3SS effector IpaH domain / Shigella T3SS effector IpaH defines / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Leucine-rich repeats, bacterial type / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Shigella T3SS effector IpaH domain / Shigella T3SS effector IpaH defines / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Leucine-rich repeats, bacterial type / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine-rich repeat domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ipaH9.8 / E3 ubiquitin-protein ligase ipaH9.8
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSeyedarabi, A. / Sullivan, J.A. / Sasakawa, C. / Pickersgill, R.W.
CitationJournal: Febs Lett. / Year: 2010
Title: A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase
Authors: Seyedarabi, A. / Sullivan, J.A. / Sasakawa, C. / Pickersgill, R.W.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IpaH9.8


Theoretical massNumber of molelcules
Total (without water)33,4601
Polymers33,4601
Non-polymers00
Water0
1
A: IpaH9.8

A: IpaH9.8


Theoretical massNumber of molelcules
Total (without water)66,9202
Polymers66,9202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3030 Å2
ΔGint-26 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.659, 92.659, 135.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein IpaH9.8


Mass: 33460.027 Da / Num. of mol.: 1
Fragment: C-terminal domain (domain swapped), residues 254-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: YSH6000 / Gene: ipaH9.8 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O85159, UniProt: Q8VSC3*PLUS, ubiquitin-protein ligase

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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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M sodium acetate trihydrate, 0.1M Tris pH 8.5, 30% polyethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.04496 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04496 Å / Relative weight: 1
ReflectionResolution: 3.2→38.46 Å / Num. all: 6131 / Num. obs: 5984 / % possible obs: 97.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 75.8 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 21.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.2 / Num. unique all: 785 / Rsym value: 0.53 / % possible all: 91.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ckd; chain A

3ckd


Resolution: 3.2→34.53 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.923 / SU B: 35.258 / SU ML: 0.562 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.62 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.311 268 4.5 %RANDOM
Rwork0.289 ---
all0.29 5841 --
obs0.29 5689 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 0 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212145
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8481.9322901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1485259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81624.407118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87115369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2091.51306
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38622079
X-RAY DIFFRACTIONr_scbond_it0.2423839
X-RAY DIFFRACTIONr_scangle_it0.4454.5822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 16 -
Rwork0.345 385 -
obs-385 90.93 %

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