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- PDB-2j0n: A proteolytically truncated form of Shigella Flexneri IpaD -

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Basic information

Entry
Database: PDB / ID: 2j0n
TitleA proteolytically truncated form of Shigella Flexneri IpaD
ComponentsINVASIN IPAD
KeywordsCELL INVASION / IPAD / T3SS / PLASMID / VIRULENCE / SHIGELLA FLEXNERI / TYPE III SECRETION
Function / homology
Function and homology information


effector-mediated activation of programmed cell death in host / extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohnson, S. / Roversi, P. / Lea, S.M.
Citation
Journal: J Biol Chem / Year: 2007
Title: Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD.
Authors: Steven Johnson / Pietro Roversi / Marianela Espina / Andrew Olive / Janet E Deane / Susan Birket / Terry Field / William D Picking / Ariel J Blocker / Edouard E Galyov / Wendy L Picking / Susan M Lea /
Abstract: Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. ...Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Limited Proteolysis and Preliminary Crystallographic Analysis of Ipad, a Component of the Shigella Flexneri Type III Secretion System
Authors: Johnson, S. / Roversi, P. / Espina, M. / Deane, J.E. / Birket, S. / Picking, W.D. / Blocker, A. / Picking, W.L. / Lea, S.M.
History
DepositionAug 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_gene_src_variant / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INVASIN IPAD
B: INVASIN IPAD


Theoretical massNumber of molelcules
Total (without water)44,2992
Polymers44,2992
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.790, 91.360, 54.910
Angle α, β, γ (deg.)90.00, 96.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2012-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.287, 0.04773, 0.95674), (0.01844, 0.9983, -0.05533), (-0.95775, 0.03352, 0.28563)
Vector: -13.40568, 7.31436, 11.2957)

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Components

#1: Protein INVASIN IPAD / IPAD


Mass: 22149.730 Da / Num. of mol.: 2 / Fragment: TRUNCATED FORM, RESIDUES 133-332
Source method: isolated from a genetically manipulated source
Details: THE TRUNCATION WAS OBTAINED BY IN-DROP CLEAVAGE BY UNKOWN PROTEASE OF A CONSTRUCT CONSISTING OF RESIDUES 15-332
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Plasmid: PET-15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18013
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TRUNCATION WAS INTRODUCED BY AN UNKNOWN PROTEASE IN THE CRYSTALLISATION DROP

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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: 2.15 Å3/Da / Density % sol: 43 %
Description: THE SEARCH MODEL FOR MOLECULAR REPLACEMENT IS AN IPAD POLYMORPH THAT WE ARE GOING TO DEPOSIT SOON.
Crystal growpH: 7
Details: 10 % (V/V) PEG 400, 0.1 M NACL, 0.1 M TRIS-HCL, PH7.0, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→42 Å / Num. obs: 24238 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: REFINED IN BUSTER-TNT BETA 1.9.2
RfactorNum. reflection
Rwork0.189 -
all0.19 22218
obs0.189 22218
Solvent computationSolvent model: BABINET SCALING / Bsol: 175 Å2 / ksol: 0.43 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 0 205 2986
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00728272
X-RAY DIFFRACTIONt_angle_deg1.27238192
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0081002
X-RAY DIFFRACTIONt_gen_planes0.0193895
X-RAY DIFFRACTIONt_it1.496282720
X-RAY DIFFRACTIONt_nbd0.076695
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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