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- PDB-7v8h: Crystal structure of LRR domain from Shigella flexneri IpaH1.4 -

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Basic information

Entry
Database: PDB / ID: 7v8h
TitleCrystal structure of LRR domain from Shigella flexneri IpaH1.4
ComponentsRING-type E3 ubiquitin transferase
KeywordsLIGASE / ubiquitin / innate immune
Function / homology
Function and homology information


modulation of process of another organism / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / protein ubiquitination / extracellular region
Similarity search - Function
Novel E3 ligase (NEL) domain 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 repeats, bacterial type / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesShigella flexneri 5a str. M90T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsLiu, J. / Wang, Y. / Pan, L.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071297 China
National Natural Science Foundation of China (NSFC)21822705 China
National Natural Science Foundation of China (NSFC)91753113 China
National Natural Science Foundation of China (NSFC)21621002 China
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri.
Authors: Liu, J. / Wang, Y. / Wang, D. / Wang, Y. / Xu, X. / Zhang, Y. / Li, Y. / Zhang, M. / Gong, X. / Tang, Y. / Shen, L. / Li, M. / Pan, L.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RING-type E3 ubiquitin transferase
B: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)53,9842
Polymers53,9842
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint4 kcal/mol
Surface area21850 Å2
Unit cell
Length a, b, c (Å)108.780, 108.780, 99.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 38 or (resid 39 and (name...
d_2ens_1(chain "B" and (resid 38 through 42 or (resid 43...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNLEUA1 - 119
d_12ens_1VALGLYA121 - 236
d_21ens_1ASNLEUB1 - 119
d_22ens_1VALGLYB123 - 238

NCS oper: (Code: givenMatrix: (-0.909535870212, -0.0948495899864, 0.40465794948), (-0.0753447108192, -0.919853403415, -0.384958297452), (0.408739128723, -0.380622216253, 0.829493250814)Vector: 62. ...NCS oper: (Code: given
Matrix: (-0.909535870212, -0.0948495899864, 0.40465794948), (-0.0753447108192, -0.919853403415, -0.384958297452), (0.408739128723, -0.380622216253, 0.829493250814)
Vector: 62.440671272, 62.6499606707, -0.728408707562)

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Components

#1: Protein RING-type E3 ubiquitin transferase


Mass: 26991.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 5a str. M90T (bacteria)
Strain: M90T / Gene: ipaH1.4 / Plasmid: pRSF-Deut1-Trx / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4 / Details: 0.1 M sodium citrate (pH 4.0), 0.8 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.456→76.919 Å / Num. obs: 21136 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 24.6 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.067 / Net I/σ(I): 14.4
Reflection shellResolution: 2.456→2.498 Å / Redundancy: 25.4 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1091 / CC1/2: 0.81 / Rpim(I) all: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSbuilt 20190606data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KH1

5kh1


Resolution: 2.46→60.82 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 1057 5 %
Rwork0.1943 20070 -
obs0.1962 21127 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.53 Å2
Refinement stepCycle: LAST / Resolution: 2.46→60.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 0 90 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063811
X-RAY DIFFRACTIONf_angle_d1.25545203
X-RAY DIFFRACTIONf_chiral_restr0.0607606
X-RAY DIFFRACTIONf_plane_restr0.0087685
X-RAY DIFFRACTIONf_dihedral_angle_d6.1595499
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.734799407111 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.570.24181370.19652592X-RAY DIFFRACTION100
2.57-2.70.34321020.22051957X-RAY DIFFRACTION75.23
2.7-2.870.2671380.21462609X-RAY DIFFRACTION100
2.87-3.090.23041380.2222611X-RAY DIFFRACTION100
3.09-3.410.2781390.21612651X-RAY DIFFRACTION100
3.41-3.880.20411160.18152202X-RAY DIFFRACTION85.98
3.91-4.910.18861380.15792624X-RAY DIFFRACTION100
4.91-60.820.23161490.20312824X-RAY DIFFRACTION99.8

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