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- PDB-7ya7: The crystal structure of IpaH1.4 LRR domain -

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Basic information

Entry
Database: PDB / ID: 7ya7
TitleThe crystal structure of IpaH1.4 LRR domain
ComponentsRING-type E3 ubiquitin transferase
KeywordsLIGASE / Shigella flexneri / Effector / IpaH1.4 / Ubiquitin ligase
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 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHiragi, K. / Nishide, A. / Takagi, K. / Iwai, K. / Kim, M. / Mizushima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24112009 Japan
CitationJournal: J.Biochem. / Year: 2023
Title: Structural insight into the recognition of the linear ubiquitin assembly complex by Shigella E3 ligase IpaH1.4/2.5.
Authors: Hiragi, K. / Nishide, A. / Takagi, K. / Iwai, K. / Kim, M. / Mizushima, T.
History
DepositionJun 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Refinement description / Category: software
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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)54,6452
Polymers54,6452
Non-polymers00
Water9,530529
1
A: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)27,3221
Polymers27,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)27,3221
Polymers27,3221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.467, 68.039, 100.260
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RING-type E3 ubiquitin transferase / Invasion plasmid antigen H1.4


Mass: 27322.393 Da / Num. of mol.: 2 / Fragment: LRR domain(substrate recognision domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 5a (bacteria) / Strain: M90T / Gene: ipaH1.4, S0283, pWR501_0283 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 50 mM imidazole (pH 8.0), 1.2 M NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 86206 / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 33.9
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4 / Num. unique obs: 8222

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B0N

5b0n


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.133 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21984 4265 5 %RANDOM
Rwork0.18543 ---
obs0.18712 80738 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.45 Å2
2---0.23 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 0 529 4150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193705
X-RAY DIFFRACTIONr_bond_other_d0.0030.023663
X-RAY DIFFRACTIONr_angle_refined_deg2.5022.0015054
X-RAY DIFFRACTIONr_angle_other_deg1.29138452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.47625.439171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.915649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1111520
X-RAY DIFFRACTIONr_chiral_restr0.1770.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214149
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02791
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_it1.8151.4111813
X-RAY DIFFRACTIONr_mcbond_other1.8151.4111812
X-RAY DIFFRACTIONr_mcangle_it2.3882.122261
X-RAY DIFFRACTIONr_mcangle_other2.3872.122262
X-RAY DIFFRACTIONr_scbond_it3.6791.8521892
X-RAY DIFFRACTIONr_scbond_other3.6781.8521893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3312.6232794
X-RAY DIFFRACTIONr_long_range_B_refined7.54714.0154530
X-RAY DIFFRACTIONr_long_range_B_other7.20112.9554240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 299 -
Rwork0.247 5656 -
obs--94.06 %

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