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- PDB-6lol: The crystal structure of full length IpaH9.8 -

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Basic information

Entry
Database: PDB / ID: 6lol
TitleThe crystal structure of full length IpaH9.8
ComponentsE3 ubiquitin-protein ligase ipaH9.8
KeywordsTRANSFERASE / E3 / IpaH9.8
Function / homology
Function and homology information


modulation of process of another organism / protein K27-linked ubiquitination / host cell cytosol / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell nucleus / 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 repeat domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ipaH9.8
Similarity search - Component
Biological speciesShigella flexneri 2002017 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYe, Y. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21907006 China
CitationJournal: Commun Biol / Year: 2020
Title: Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8.
Authors: Ye, Y. / Xiong, Y. / Huang, H.
History
DepositionJan 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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
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: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)59,9231
Polymers59,9231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25070 Å2
2
A: E3 ubiquitin-protein ligase ipaH9.8

A: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)119,8452
Polymers119,8452
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2180 Å2
ΔGint-2 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.640, 122.250, 149.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein E3 ubiquitin-protein ligase ipaH9.8 / Invasion plasmid antigen ipaH9.8 / RING-type E3 ubiquitin transferase ipaH9.8


Mass: 59922.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2002017 (bacteria) / Strain: 2002017 / Gene: ipaH9.8, SFxv_5076 / Production host: Escherichia coli (E. coli)
References: UniProt: D2AJU0, RING-type E3 ubiquitin transferase

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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: 4.09 Å3/Da / Density % sol: 73.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.0M NaCl, 0.1M Na Citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→86.91 Å / Num. obs: 25746 / % possible obs: 99.46 % / Redundancy: 6.6 % / Biso Wilson estimate: 81.01 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.0873 / Net I/σ(I): 15.74
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.56 / Num. unique obs: 2524 / CC1/2: 0.862 / CC star: 0.962 / % possible all: 99.41

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B0T

5b0t


Resolution: 2.75→86.91 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 1318 5.13 %
Rwork0.2461 24385 -
obs0.248 25703 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.09 Å2 / Biso mean: 102.7644 Å2 / Biso min: 40.08 Å2
Refinement stepCycle: final / Resolution: 2.75→86.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 0 0 3460
Num. residues----466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.860.37421370.4044251399
2.86-2.990.33941580.31962664100
2.99-3.150.38491430.29512701100
3.15-3.340.28881490.26992683100
3.35-3.60.26241500.2519266999
3.6-3.970.24961230.21572726100
3.97-4.540.23241560.2112705100
4.54-5.720.25641470.23122747100
5.72-86.910.321550.25283699

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