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- PDB-5kh1: Shigella flexneri Effector IpaH1880 -

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Basic information

Entry
Database: PDB / ID: 5kh1
TitleShigella flexneri Effector IpaH1880
ComponentsInvasion plasmid antigen
KeywordsLIGASE / Shigella / Effector / E3 Ligase / Ubiquitin
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNishide, A. / Mizushima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grant-in-Aid for Scientific Research (B)15H04341 Japan
Grant-in-Aid for JSPS Fellows14J10879 Japan
CitationJournal: To Be Published
Title: Shigella flexneri Effector IpaH1880
Authors: Nishide, A. / Mizushima, T.
History
DepositionJun 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Invasion plasmid antigen


Theoretical massNumber of molelcules
Total (without water)66,8601
Polymers66,8601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29520 Å2
Unit cell
Length a, b, c (Å)56.316, 80.058, 298.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Invasion plasmid antigen


Mass: 66859.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH_4, SF1880 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q83R64

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1%(w/v) Tacsimate pH6.0 100mM Bis-Tris/HCl pH6.5 16% 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: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 9062 / % possible obs: 92.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 92.8779608153 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.533 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
BUCCANEERmodel building
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVR

3cvr


Resolution: 3.4→44.011 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 471 5.22 %RANDOM
Rwork0.2388 ---
obs0.2423 9019 92.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→44.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 0 0 0 4421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114514
X-RAY DIFFRACTIONf_angle_d1.7116147
X-RAY DIFFRACTIONf_dihedral_angle_d19.7132750
X-RAY DIFFRACTIONf_chiral_restr0.07697
X-RAY DIFFRACTIONf_plane_restr0.009809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4003-3.89210.36321410.29872579X-RAY DIFFRACTION86
3.8921-4.90260.34881550.25342837X-RAY DIFFRACTION93
4.9026-44.01460.26251750.21163132X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.4278 Å / Origin y: -6.016 Å / Origin z: -38.3649 Å
111213212223313233
T0.7069 Å2-0.065 Å2-0.0321 Å2-0.7777 Å2-0.0258 Å2--0.5475 Å2
L0.1978 °2-0.0744 °2-0.0535 °2-1.1174 °2-1.6377 °2--2.0759 °2
S-0.0182 Å °0.4869 Å °-0.0352 Å °-0.3856 Å °-0.0041 Å °0.0103 Å °0.4116 Å °-0.0994 Å °-0.001 Å °
Refinement TLS groupSelection details: all

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