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- PDB-5b0n: Structure of Shigella effector LRR domain -

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Basic information

Entry
Database: PDB / ID: 5b0n
TitleStructure of Shigella effector LRR domain
ComponentsE3 ubiquitin-protein ligase ipaH9.8
KeywordsLIGASE / effector / ubiquitin ligase / LRR domain
Function / homology
Function and homology information


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 ...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
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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ipaH9.8
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTakagi, K. / Sasakawa, C. / Kim, M. / Mizushima, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
The Ministry of Education, Culture, Sports, Science and Technology of Japan23000012 Japan
The Ministry of Education, Culture, Sports, Science and Technology of Japan24112009 Japan
The Ministry of Education, Culture, Sports, Science and Technology of Japan15H01174 Japan
The Ministry of Education, Culture, Sports, Science and Technology of Japan15H04341 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of the substrate-recognition domain of the Shigella E3 ligase IpaH9.8
Authors: Takagi, K. / Kim, M. / Sasakawa, C. / Mizushima, T.
History
DepositionNov 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)50,7552
Polymers50,7552
Non-polymers00
Water2,576143
1
A: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)25,3781
Polymers25,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)25,3781
Polymers25,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.792, 66.192, 105.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25377.514 Da / Num. of mol.: 2 / Fragment: UNP residues 22-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH9.8, CP0226, pWR501_0234, SFLP090 / Plasmid: pCold1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8VSC3, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS pH5.5, 0.2M Lithium Sulfate monohydrate, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39927 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 49.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.472 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.206 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1996 5 %RANDOM
Rwork0.2096 ---
obs0.212 37748 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.7 Å2 / Biso mean: 30.486 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 0 143 3626
Biso mean---31.87 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023672
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9925029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27924.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67415640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1221528
X-RAY DIFFRACTIONr_chiral_restr0.1330.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0222828
LS refinement shellResolution: 1.803→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 133 -
Rwork0.262 2523 -
all-2656 -
obs--98.59 %

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