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- PDB-7ya8: The crystal structure of IpaH2.5 LRR domain -

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Basic information

Entry
Database: PDB / ID: 7ya8
TitleThe crystal structure of IpaH2.5 LRR domain
ComponentsRING-type E3 ubiquitin transferase
KeywordsLIGASE / Shigella flexneri / Effector / IpaH2.5 / 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 / cytoplasm
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: 3.4 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 1.1Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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)54,6732
Polymers54,6732
Non-polymers00
Water181
1
A: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)27,3361
Polymers27,3361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RING-type E3 ubiquitin transferase


Theoretical massNumber of molelcules
Total (without water)27,3361
Polymers27,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.785, 137.686, 163.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RING-type E3 ubiquitin transferase / Invasion plasmid antigen H2.5


Mass: 27336.420 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: ipaH2.5, S0056, EKN05_023760, pWR501_0056 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7BEH4, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 6.74 Å3/Da / Density % sol: 81.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M succinic acid pH 6.6, 18.8% (w/v) polyethylene glycol (PEG)3350

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 22003 / % possible obs: 96 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.82 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 22
Reflection shellResolution: 3.301→3.419 Å / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1436 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YA7

7ya7


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.512 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 1123 5.1 %RANDOM
Rwork0.19796 ---
obs0.20039 20798 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.278 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 0 1 3810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193898
X-RAY DIFFRACTIONr_bond_other_d00.023830
X-RAY DIFFRACTIONr_angle_refined_deg0.6772.0015318
X-RAY DIFFRACTIONr_angle_other_deg0.51938842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3045478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83725.531179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03915678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5781520
X-RAY DIFFRACTIONr_chiral_restr0.0490.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0214389
X-RAY DIFFRACTIONr_gen_planes_other00.02831
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_it9.8515.9261918
X-RAY DIFFRACTIONr_mcbond_other9.855.9261917
X-RAY DIFFRACTIONr_mcangle_it13.7658.9072394
X-RAY DIFFRACTIONr_mcangle_other13.7638.9082395
X-RAY DIFFRACTIONr_scbond_it11.1686.5161980
X-RAY DIFFRACTIONr_scbond_other11.1666.5161981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.5489.5432925
X-RAY DIFFRACTIONr_long_range_B_refined18.09749.864387
X-RAY DIFFRACTIONr_long_range_B_other18.09549.8644388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.46 Å
RfactorNum. reflection% reflection
Rfree0.333 50 -
Rwork0.311 747 -
obs--47.72 %

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