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- PDB-2jaa: SeMet substituted Shigella Flexneri Ipad -

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Basic information

Entry
Database: PDB / ID: 2jaa
TitleSeMet substituted Shigella Flexneri Ipad
ComponentsINVASIN IPAD
KeywordsCELL INVASION / IPAD / T3SS / SEMET / INVASIN / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.1 Å
AuthorsJohnson, S. / Roversi, P. / Espina, M. / Olive, A. / Deane, J.E. / Birket, S. / Field, T. / Picking, W.D. / Blocker, A.J. / Galyov, E.E. ...Johnson, S. / Roversi, P. / Espina, M. / Olive, A. / Deane, J.E. / Birket, S. / Field, T. / Picking, W.D. / Blocker, A.J. / Galyov, E.E. / Picking, W.L. / Lea, S.M.
CitationJournal: 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.
History
DepositionNov 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INVASIN IPAD
B: INVASIN IPAD


Theoretical massNumber of molelcules
Total (without water)47,4792
Polymers47,4792
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)137.838, 44.484, 100.310
Angle α, β, γ (deg.)90.00, 107.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.71843, -0.12847, -0.68364), (-0.10344, -0.9916, 0.07763), (-0.68787, 0.01494, -0.72568)
Vector: -0.65075, -25.94786, 1.48101)

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Components

#1: Protein INVASIN IPAD


Mass: 23739.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 121-332
Source method: isolated from a genetically manipulated source
Details: PROTELYSIS PRODUCT. SEMET SUBSTITUTED / Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: 301 / Variant: SEROTYPE 2A / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18013
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.78 Å3/Da / Density % sol: 67.17 %
Crystal growpH: 8.5
Details: 30%(V/V) PEG 400, 0.1 M TRIS-HCL PH 8.5, 0.2 M SODIUM CITRATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→33.9 Å / Num. obs: 62274 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SOLOMONmodel building
TNT5.6.1refinement
SCALAdata scaling
SHELXCDphasing
SHELXDphasing
SHARPphasing
SOLOMONphasing
RESOLVEphasing
ARP/wARPphasing
HELIXBUILDphasing
RefinementMethod to determine structure: OTHER / Resolution: 3.1→34 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTEGEO
Details: REFINED IN BUSTER-TNT BETA 1.9.3 WAS USED AS A MOLECULAR REPLACEMENT MODEL FOR DETERMINING THE STRUCTURES OF PDB ENTRIES 2J0N, 2J0O
RfactorNum. reflection% reflectionSelection details
Rfree0.2755 502 5 %0.2628
Rwork0.2621 ---
all0.2628 ---
obs0.2621 9700 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 47 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 3.1→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 0 8 2767
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00228043
X-RAY DIFFRACTIONt_angle_deg0.55437814
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006902
X-RAY DIFFRACTIONt_gen_planes0.0163815
X-RAY DIFFRACTIONt_it0.618280420
X-RAY DIFFRACTIONt_nbd0.02211110
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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