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- PDB-8v7s: IpaD (122-321) Apo Structure -

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Basic information

Entry
Database: PDB / ID: 8v7s
TitleIpaD (122-321) Apo Structure
ComponentsInvasin IpaD
KeywordsCELL INVASION / Type Three Secretion System / T3SS / T3SA / Shigella / Pi helix / Deoxycholate bound
Function / homologyeffector-mediated activation of host programmed cell death by symbiont / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 Å
AuthorsBarker, S.A. / Dickenson, N.E. / Johnson, S.J. / Morales, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and functional characterization of the IpaD pi-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.
Authors: Barker, S.A. / Bernard, A.R. / Morales, Y. / Johnson, S.J. / Dickenson, N.E.
History
DepositionDec 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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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)44,4842
Polymers44,4842
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-13 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.631, 44.015, 92.509
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Invasin IpaD / Invasion Plasmid Antigen D


Mass: 22241.812 Da / Num. of mol.: 2 / Fragment: residues 122-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 0.018 - 0.02 M Magnesium Chloride Hexahydrate, 20% w/v Poly (acrylic acid sodium salt) 5100, 0.3 mM Deoxycholate acid sodium salt

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13359 / % possible obs: 96.6 % / Redundancy: 5 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.056 / Rrim(I) all: 0.13 / Χ2: 0.989 / Net I/σ(I): 5.6 / Num. measured all: 66496
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.70.47711920.8240.9510.2550.5460.98989
2.8-2.914.10.42113140.8780.9670.220.4790.98794.1
2.91-3.044.50.37113000.9290.9810.1880.4191.00796
3.04-3.24.60.31213220.9370.9840.1550.350.98797.1
3.2-3.45.40.24713560.9660.9910.1150.2740.98498.6
3.4-3.665.50.19813820.9680.9920.0920.2190.98399.4
3.66-4.035.40.14913320.9850.9960.070.1661.00197.4
4.03-4.625.60.09313480.9920.9980.0420.1020.98398.3
4.62-5.815.50.08113900.9950.9990.0370.090.9898.2
5.81-505.30.05714230.99810.0270.0630.99297.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.708→45.89 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 669 5.02 %
Rwork0.2251 --
obs0.2281 13325 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.708→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 23 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023057
X-RAY DIFFRACTIONf_angle_d0.5014135
X-RAY DIFFRACTIONf_dihedral_angle_d2.3821843
X-RAY DIFFRACTIONf_chiral_restr0.037461
X-RAY DIFFRACTIONf_plane_restr0.003534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7085-2.91760.39311240.32312276X-RAY DIFFRACTION87
2.9176-3.21110.30911310.29012506X-RAY DIFFRACTION96
3.2111-3.67560.34151390.26282618X-RAY DIFFRACTION99
3.6756-4.63010.23351340.19622576X-RAY DIFFRACTION98
4.6301-45.890.26791410.18822680X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.19840.01823.46532.57320.98833.2560.06620.35060.1354-0.6535-0.2266-0.0117-0.24090.02380.12190.61760.00790.11260.3812-0.05130.353-21.23431.5736-49.8434
20.6956-0.02970.08331.27580.02716.73770.7947-0.0458-0.64180.5893-0.0746-0.51241.82031.2546-0.31870.77190.0589-0.17930.53110.05550.45190.198-3.601-9.9161
35.51772.1755-0.21794.78911.44557.4929-0.41230.07950.6614-0.96660.44760.02430.10510.60130.08940.483-0.0606-0.03820.40790.04320.2996-2.26795.7474-28.6477
42.05731.9232.65381.75711.98737.50250.1641-0.75460.13150.438-0.2612-0.14230.2358-0.03620.11330.51160.0041-0.00530.396-0.01460.3153-6.36143.6654-14.0566
51.3918-1.0445-0.6241.19172.14999.2216-0.07740.10880.1095-0.4527-0.26080.3392-0.9350.1340.17640.4431-0.09220.02580.19920.02540.386-32.891114.1031-33.8656
62.73250.5527-1.89145.30292.20254.04860.1584-1.0692-0.05011.1032-0.1496-0.2418-0.5663-0.03510.26980.633-0.01970.0570.8244-0.15670.5996-38.157621.10135.543
78.1355-0.60382.23994.1319-0.90250.9528-0.3363-0.06670.2194-0.0496-0.0730.2065-0.1007-0.44860.31920.5481-0.027-0.00540.41120.01450.3215-45.223211.6161-22.8791
82.6972-0.4556-2.76982.1522-0.05238.0374-0.0935-0.3549-0.0950.2876-0.0730.0280.5240.31060.1110.38970.0242-0.02540.2945-0.05010.3643-32.43210.8959-11.1562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 124 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 318 )
5X-RAY DIFFRACTION5chain 'B' and (resid 124 through 173 )
6X-RAY DIFFRACTION6chain 'B' and (resid 174 through 205 )
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 250 )
8X-RAY DIFFRACTION8chain 'B' and (resid 251 through 319 )

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