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- PDB-8v5e: IpaD (122-321) Pi-helix Mutant (delta Q148) Bound to Deoxycholate -

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Basic information

Entry
Database: PDB / ID: 8v5e
TitleIpaD (122-321) Pi-helix Mutant (delta Q148) Bound to Deoxycholate
ComponentsInvasin IpaD
KeywordsCELL INVASION / T3SS / Shigella / Pi-helix / Deoxycholate
Function / homologyeffector-mediated activation of programmed cell death in host / 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: 2.2 Å
AuthorsBarker, S.A. / Dickenson, N.E. / Johnson, S.J.
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
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5845
Polymers43,7072
Non-polymers8773
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.612, 70.313, 171.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Invasin IpaD


Mass: 21853.375 Da / Num. of mol.: 2 / Mutation: Q148 deleted
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: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 59.03 %
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: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 27135 / % possible obs: 97.3 % / Redundancy: 12 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Χ2: 1.016 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.70.5724500.8460.9580.2160.6131.06689.8
2.28-2.379.90.48425790.9290.9820.1540.5091.02594.7
2.37-2.4812.70.33826940.9730.9930.0960.3511.0398.6
2.48-2.61130.23127590.9880.9970.0660.2411.01899.3
2.61-2.7712.60.1627360.9940.9980.0460.1661.00899.3
2.77-2.9912.80.11126490.9970.9990.0320.1150.99296.3
2.99-3.2913.20.0827590.9980.9990.0230.0831.0399.5
3.29-3.7612.70.05927240.99810.0170.0610.99797
3.76-4.7413.30.04928370.99910.0140.0511.01399.9
4.74-3512.10.04229480.99910.0130.0441.0197.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.649 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1343 5 %
Rwork0.197 --
obs0.1988 26856 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 62 91 3183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033147
X-RAY DIFFRACTIONf_angle_d0.5794271
X-RAY DIFFRACTIONf_dihedral_angle_d5.0081870
X-RAY DIFFRACTIONf_chiral_restr0.041486
X-RAY DIFFRACTIONf_plane_restr0.003540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27870.3231200.26282291X-RAY DIFFRACTION91
2.2787-2.36990.31811300.25582467X-RAY DIFFRACTION95
2.3699-2.47770.26951330.23432526X-RAY DIFFRACTION99
2.4777-2.60830.26571370.22462592X-RAY DIFFRACTION99
2.6083-2.77170.30121350.2282559X-RAY DIFFRACTION99
2.7717-2.98560.25681320.23372506X-RAY DIFFRACTION97
2.9856-3.28580.25641360.22692601X-RAY DIFFRACTION99
3.2858-3.76080.23031360.20212570X-RAY DIFFRACTION97
3.7608-4.73630.22121390.16422655X-RAY DIFFRACTION100
4.7363-34.6490.1771450.17092746X-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)
10.7991-0.0687-0.5717.31887.91698.84280.14860.0303-0.16480.270.3437-0.69530.31070.1807-0.49920.29330.0511-0.1110.4397-0.03440.448623.0506-6.0253-20.1835
21.87920.48241.02213.60371.50473.7320.3146-0.7461-0.11932.1301-0.093-0.23251.5262-0.0648-0.23670.9686-0.0099-0.17050.6759-0.04790.488818.7505-15.6919-14.1319
30.92372.08132.0916.20956.76367.5525-0.18430.1235-0.0487-0.35350.180.1506-0.3230.29090.00350.28770.0473-0.03830.4063-0.05140.379317.6365-3.1882-24.5869
41.6740.5242.59681.08561.50748.59470.0219-0.30330.26560.0426-0.07820.1448-0.1406-0.44110.06740.3210.0217-0.00530.2698-0.03840.36943.340619.3409-20.4357
57.5279-2.2888-0.89878.75753.98752.2147-0.07980.44950.0528-1.022-0.13850.165-1.1146-0.02620.30590.3706-0.0268-0.0590.32610.12580.3871-3.933218.897-52.2023
62.44811.95923.1914.52895.12558.616-0.1470.3640.372-0.23980.2514-0.2722-1.00740.7462-0.08620.4051-0.0577-0.04420.46720.05580.57056.751826.0888-37.1637
70.39720.51522.4744-0.03370.98723.18190.15920.2128-0.0449-0.01770.01870.01350.51580.4517-0.13050.40430.1128-0.05380.4866-0.0680.41027.825911.4246-28.2107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 205 )
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 262 )
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 320 )
4X-RAY DIFFRACTION4chain 'B' and (resid 126 through 179 )
5X-RAY DIFFRACTION5chain 'B' and (resid 180 through 206 )
6X-RAY DIFFRACTION6chain 'B' and (resid 207 through 271 )
7X-RAY DIFFRACTION7chain 'B' and (resid 272 through 320 )

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